# HG changeset patch
# User bgruening
# Date 1589197507 14400
# Node ID 27396311a314fea7e42cc4bbc5de60e4bb739941
# Parent  3c3cd68d6d5a29182f07752cbc72c2adfa409d4e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"

diff -r 3c3cd68d6d5a -r 27396311a314 macros.xml
--- a/macros.xml	Thu Apr 16 05:29:02 2020 -0400
+++ b/macros.xml	Mon May 11 07:45:07 2020 -0400
@@ -25,12 +25,12 @@
     </token>
 
 
-    <xml name="output_pipeline_macro">
-        <data name="out_file" from_work_dir="output" format="txt"/>
+    <xml name="output_pipeline_param">
+        <data name="output_pipeline" from_work_dir="output.cppipe" format="txt"/>
     </xml>
 
 
-    <xml name="input_pipeline_macro">
+    <xml name="input_pipeline_param">
         <param name="input_pipeline" type="data" format="data" label="Select the input CellProfiler pipeline"/>
     </xml>
 
@@ -81,25 +81,13 @@
 
 
     <xml name="test_input_pipeline_param">
-        <param name="input_pipeline" value="common.txt" />
-    </xml>
-
-
-    <xml name="test_out_file" token_file="common.txt">
-        <output name="out_file" ftype="txt" file="@FILE@" lines_diff="0"/>
+        <param name="input_pipeline" value="common.cppipe" />
     </xml>
 
 
-    <xml name="help" token_module="common">
-        <help>
-            This tool appends the inputs of the @MODULE@ module to an existing pipeline file (.cppipe)
-
-            Input: existing pipeline file
-
-            Output: new pipeline file
-
-            Combine this tool with "Common" tool and "CellProfiler" tool together to run the current module alone.
-        </help>
+    <xml name="test_out_file" token_file="common.cppipe">
+        <output name="output_pipeline" ftype="txt" file="@FILE@" lines_diff="0"/>
     </xml>
+    
 </macros>
 
diff -r 3c3cd68d6d5a -r 27396311a314 starting_modules.py
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/starting_modules.py	Mon May 11 07:45:07 2020 -0400
@@ -0,0 +1,227 @@
+import json
+import sys
+import os
+
+FOURSPACES = "    "
+
+input_json_path = sys.argv[1]
+
+params = json.load(open(input_json_path, "r"))
+
+
+def write_images():
+    filter_images = params['images']['filter_images']
+
+    _str = "\nImages:[module_num:1|svn_version:\\'Unknown\\'|variable_revision_number:2|show_window:False|notes:\\x5B\\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]\n"
+    _str += FOURSPACES+":\n"
+    _str += FOURSPACES + "Filter images?:%s\n" % filter_images
+    _str += FOURSPACES + "Select the rule criteria:and (extension does isimage) (directory doesnot startwith \".\")\n"
+
+    return _str
+
+
+def write_metadata():
+    metadata_extraction = params['metadata']['con_metadata_extraction']
+    extract = metadata_extraction['extract']
+
+    if 'extraction_method' in metadata_extraction:
+        method_count = len(metadata_extraction['extraction_method'])
+    else:
+        method_count = 1
+
+    _str = "\nMetadata:[module_num:2|svn_version:\\'Unknown\\'|variable_revision_number:4|show_window:False|notes:\\x5B\\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]\n"
+    _str += FOURSPACES + "Extract metadata?:%s\n" % extract
+
+    if extract == "No":
+        _str += FOURSPACES + "Metadata data type:Text\n"
+        _str += FOURSPACES + "Metadata types:{}\n"
+        _str += FOURSPACES + "Extraction method count:%d\n" % method_count
+        _str += FOURSPACES + "Metadata extraction method:Extract from file/folder names\n"
+        _str += FOURSPACES + "Regular expression to extract from file name:^(?P<Plate>.*)_(?P<Well>\x5BA-P\x5D\x5B0-9\x5D{2})_s(?P<Site>\x5B0-9\x5D)_w(?P<ChannelNumber>\x5B0-9\x5D)\n"
+        _str += FOURSPACES + "Regular expression to extract from folder name:(?P<Date>\x5B0-9\x5D{4}_\x5B0-9\x5D{2}_\x5B0-9\x5D{2})$\n"
+        _str += FOURSPACES + "Extract metadata from:All images\n"
+        _str += FOURSPACES + "Select the filtering criteria:and (file does contain \"\")\n"
+        _str += FOURSPACES + "Metadata file location:\n"
+        _str += FOURSPACES + "Match file and image metadata:\x5B\x5D\n"
+        _str += FOURSPACES + "Use case insensitive matching?:No\n"
+    else:
+        _str += FOURSPACES + "Metadata data type:Text\n"  #default Text,not possible to select in Galaxy
+        _str += FOURSPACES + "Metadata types:{}\n"
+        _str += FOURSPACES + "Extraction method count:%d\n" % method_count
+
+        for methods in metadata_extraction["extraction_method"]:
+            _str += FOURSPACES + "Metadata extraction method:%s\n" % methods["metadata_extraction_method"]
+            _str += FOURSPACES + "Metadata source:%s\n" % methods["con_metadata_source"]["metadata_source"]
+
+            if "file_name_regex" in methods["con_metadata_source"]:
+                file_regex = methods["con_metadata_source"]["file_name_regex"]
+                folder_regex = "(?P<folderField1>.*)"
+            elif "folder_name_regex" in methods["con_metadata_source"]:
+                file_regex = "(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)"
+                folder_regex = methods["con_metadata_source"]["folder_name_regex"]
+            else:
+                # default regex
+                file_regex = "(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)"
+                folder_regex = "(?P<folderField1>.*)"
+
+            _str += FOURSPACES + "Regular expression to extract from file name:%s\n" % file_regex
+            _str += FOURSPACES + "Regular expression to extract from folder name:%s\n" % folder_regex
+
+            _str += FOURSPACES + "Extract metadata from:%s\n" % methods["con_metadata_extract_from"]["extract_metadata_from"]
+
+            if methods["con_metadata_extract_from"]["extract_metadata_from"] == "Images matching a rule":
+                rule_str =""
+                for r in methods["con_metadata_extract_from"]["r_match"]:
+                    if r["con_match"]["rule_type"] == "extension":
+                        rule_str += " (" + r["con_match"]["rule_type"] + " " + r["con_match"]["operator"] + " " + \
+                                    r["con_match"]["match_type"]+")"
+                    else:
+                        rule_str +=" (" + r["con_match"]["rule_type"] + " " + r["con_match"]["operator"] + " " +\
+                                   r["con_match"]["contain"] + " \"" + r["con_match"]["match_value"] +"\")"
+
+
+                _str += FOURSPACES + "Select the filtering criteria:" + methods["con_metadata_extract_from"]["match_all_any"] + rule_str +"\n"
+            else:
+                _str += FOURSPACES + "Select the filtering criteria:and (file does contain \"\")\n" #this line is required even if it's not used
+
+            _str += FOURSPACES + "Metadata file location:\n"
+            _str += FOURSPACES + "Match file and image metadata:\x5B\x5D\n"
+            _str += FOURSPACES + "Use case insensitive matching?:No\n"
+
+    return _str
+
+
+def write_nameandtypes():
+    nameandtypes = params['nameandtypes']
+    assign_a_name = nameandtypes['con_assign_a_name_to']['assign_a_name_to']
+
+    if "con_select_image_type" in nameandtypes['con_assign_a_name_to']:
+        con_set_intensity = nameandtypes['con_assign_a_name_to']['con_select_image_type']['con_set_intensity']
+        max_intensity = con_set_intensity['maximum_intensity'] if "maximum_intensity" in con_set_intensity else 255.0
+    else:
+        max_intensity = 255.0
+
+    pixel_space = nameandtypes['pixel_space']
+
+    rule_count = len(nameandtypes['con_assign_a_name_to']['r_match_rule']) if "r_match_rule" in nameandtypes['con_assign_a_name_to'] else 1
+
+    process_3d = nameandtypes['pixel_space']['process_3d']
+    x_spacing = 1.0 if "x_spacing" not in pixel_space else pixel_space["x_spacing"]
+    y_spacing = 1.0 if "y_spacing" not in pixel_space else pixel_space["y_spacing"]
+    z_spacing = 1.0 if "z_spacing" not in pixel_space else pixel_space["z_spacing"]
+
+    _str = "\nNamesAndTypes:[module_num:3|svn_version:\\'Unknown\\'|variable_revision_number:8|show_window:False|notes:\\x5B\\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\\'\\x5D|batch_state:array(\\x5B\\x5D, dtype=uint8)|enabled:True|wants_pause:False]\n"
+
+    _str += FOURSPACES + "Assign a name to:%s\n" % assign_a_name
+
+    if assign_a_name == "All images":
+        _str += FOURSPACES + "Select the image type:%s\n" % nameandtypes['con_assign_a_name_to']['con_select_image_type']['select_image_type']
+        _str += FOURSPACES + "Name to assign these images:%s\n" % nameandtypes['con_assign_a_name_to']['name_to_assign']
+        _str += FOURSPACES + "Match metadata:[]\n"
+
+        _str += FOURSPACES + "Image set matching method:Order\n"
+        _str += FOURSPACES + "Set intensity range from:%s\n" % con_set_intensity['set_intensity_range_from']
+        _str += FOURSPACES + "Assignments count:%s\n" % rule_count
+        _str += FOURSPACES + "Single images count:0\n"
+        _str += FOURSPACES + "Maximum intensity:%.1f\n" % max_intensity
+        _str += FOURSPACES + "Process as 3D?:%s\n" % process_3d
+
+    else:
+        #the below lines are not relevant to "images matching rules", but needed in pipeline file
+        _str += FOURSPACES + "Select the image type:Grayscale image\n"
+        _str += FOURSPACES + "Name to assign these images:DNA\n"
+        _str += FOURSPACES + "Match metadata:[]\n"
+
+        _str += FOURSPACES + "Image set matching method:%s\n" % nameandtypes['con_assign_a_name_to']['matching_method']
+        _str += FOURSPACES + "Set intensity range from:Image metadata\n"
+        _str += FOURSPACES + "Assignments count:%d\n" % rule_count
+        _str += FOURSPACES + "Single images count:0\n"
+        _str += FOURSPACES + "Maximum intensity:%.1f\n" % max_intensity
+        _str += FOURSPACES + "Process as 3D?:%s\n" % process_3d
+
+    _str += FOURSPACES + "Relative pixel spacing in X:%.1f\n" % x_spacing
+    _str += FOURSPACES + "Relative pixel spacing in Y:%.1f\n" % y_spacing
+    _str += FOURSPACES + "Relative pixel spacing in Z:%.1f\n" % z_spacing
+
+    if assign_a_name == "Images matching rules":
+        for rule in nameandtypes["con_assign_a_name_to"]["r_match_rule"]:
+
+            rule_str = ""
+            if len(rule["r_match"]) >0 :
+                for r in rule["r_match"]:
+                        if r["con_match"]["rule_type"] == "file" or r["con_match"]["rule_type"] == "directory":
+                            rule_str += " (" + r["con_match"]["rule_type"] + " "+r["con_match"]["operator"]+" "+\
+                                        r["con_match"]["contain"]+" \"" + r["con_match"]["match_value"] +"\")"
+                        else:
+                            rule_str += " ("+ r["con_match"]["rule_type"] + " " + r["con_match"]["operator"] + " " + \
+                                        r["con_match"]["match_type"] + ")"
+            else:
+                rule_str = " (file does contain \"\")"  #need to have a value even if it is not used
+
+            _str += FOURSPACES + "Select the rule criteria:" + rule["match_all_any"] + rule_str +"\n"
+
+            img_or_obj = rule["con_select_image_type"]["select_image_type"]
+
+            if img_or_obj == "Objects":
+                _str += FOURSPACES + "Name to assign these images:DNA\n"
+                _str += FOURSPACES + "Name to assign these objects:%s\n" % rule["con_select_image_type"]["name_to_assign"]
+            else:
+                _str += FOURSPACES + "Name to assign these images:%s\n" % rule["con_select_image_type"]["name_to_assign"]
+                _str += FOURSPACES + "Name to assign these objects:Cell\n"
+
+            _str += FOURSPACES + "Select the image type:%s\n" % img_or_obj
+
+
+            intensity_range="Image metadata" #default value
+            if img_or_obj == "Grayscale image" or img_or_obj == "Color image":
+                intensity_range = rule["con_select_image_type"]["con_set_intensity"]["set_intensity_range_from"]
+
+            _str += FOURSPACES + "Set intensity range from:%s\n" % intensity_range
+
+            if intensity_range == "Manual":
+                _str += FOURSPACES + "Maximum intensity:%s\n" % rule["con_select_image_type"]["con_set_intensity"]["maximum_intensity"]
+            else:
+                _str += FOURSPACES + "Maximum intensity:255.0\n"
+
+
+    return _str
+
+
+def write_groups():
+    groups = params['groups']
+
+    _str = "\nGroups:[module_num:4|svn_version:\\'Unknown\\'|variable_revision_number:2|show_window:False|notes:\\x5B\\\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\\'\\x5D|batch_state:array(\\x5B\\x5D, dtype=uint8)|enabled:True|wants_pause:False]\n"
+
+    group_images =  groups["con_groups"]["group_images"]
+
+    _str += FOURSPACES + "Do you want to group your images?:%s\n" % group_images
+    _str += FOURSPACES + "grouping metadata count:1\n"
+
+    if group_images == "Yes":
+        _str += FOURSPACES + "Metadata category:%s\n" % groups["con_groups"]["group_category"]
+    else:
+        _str += FOURSPACES + "Metadata category:None\n"
+
+    return _str
+
+
+with open("output.cppipe", "w") as f:
+    headers = ["CellProfiler Pipeline: http://www.cellprofiler.org\n",
+               "Version:3\n",
+               "DateRevision:319\n",
+               "GitHash:\n",
+               "ModuleCount:4\n",
+               "HasImagePlaneDetails:False",
+               "\n"]
+
+    f.writelines(headers)
+
+    img_str = write_images()
+    metadata_str = write_metadata()
+    nameandtypes_str = write_nameandtypes()
+    groups_str = write_groups()
+
+    output_str = img_str + metadata_str + nameandtypes_str + groups_str
+
+    f.write(output_str)
+    f.close()
\ No newline at end of file
diff -r 3c3cd68d6d5a -r 27396311a314 starting_modules.xml
--- a/starting_modules.xml	Thu Apr 16 05:29:02 2020 -0400
+++ b/starting_modules.xml	Mon May 11 07:45:07 2020 -0400
@@ -1,418 +1,78 @@
-<tool id="cp_common" name="Starting modules" version="@CP_VERSION@">
+<tool id="cp_common" name="Starting Modules" version="@CP_VERSION@">
     <description>load images and metadata into CellProfiler (Images, Metadata, NamesAndTypes, Groups)</description>
     <macros>
         <import>macros.xml</import>
-        <xml name="image_type_condition"> 
-            <conditional name="con_set_intensity">
-                <param name="set_intensity_range_from" type="select" label="Set intensity range from">
-                    <option value="Image metadata">Image metadata</option>
-                    <option value="Image bit-depth">Image bit-depth</option>
-                    <option value="Manual">Manual</option>
-                </param>
-                <when value="Manual">
-                    <param name="maximum_intensity" type="float" value="255.0" label="Maximum intensity"/>
-                </when>
-                <when value="Image metadata" />
-                <when value="Image bit-depth" />               
-            </conditional>
-        </xml>
-        <xml name="name_type_rule_matching_file">
-            <param name="operator" type="select">
-                <option value="does">Does</option>
-                <option value="doesnot">Does not</option>
-            </param>
-            <param name="contain" type="select">
-                <option value="contain">Contain</option>
-                <option value="Contain regular expression">Contain regular expression</option>
-                <option value="startwith">Start with</option>
-                <option value="endwith">End with</option>
-                <option value="Exactly match">Exactly match</option>
-            </param>
-            <param name="match_value" type="text"/>
-        </xml>
-        <xml name="image_matching_rules">
-            <repeat name="r_match_rule" title="Rules">
-                <param name="match_all_any" type="select" display="radio" label="Match the following rules">
-                    <option value="and">All</option>
-                    <option value="or">Any</option>
-                </param>
-                <conditional name="con_match">
-                      <param name="rule_type" type="select" label="Select rule criteria">
-                          <option value="file">File</option>
-                          <option value="directory">Directory</option>
-                          <option value="extension">Extension</option>
-                          <option value="image">Image</option>
-                          <option value="metadata">Metadata</option>
-                      </param>
-                      <when value="file">
-                          <expand macro="name_type_rule_matching_file"/>
-                      </when>
-                      <when value="directory">
-                          <expand macro="name_type_rule_matching_file"/>
-                      </when>
-                      <when value="extension" />
-                      <when value="image"/>
-                      <when value="metadata"/>
-                </conditional>
-                <param name="name_to_assign" label="Name to assign these images" type="text" />
-                <conditional name="con_select_image_type">
-                    <param name="select_image_type" type="select" label="Select the image type">
-                        <option value="Grayscale image">Grayscale image</option>
-                        <option value="Color image">Color image</option>
-                        <option value="Binary mask">Binary mask</option>
-                    </param>
-                    <when value ="Grayscale image">
-                        <expand macro="image_type_condition" />
-                    </when>
-                    <when value="Color image">
-                        <expand macro="image_type_condition" />
-                    </when>
-                    <when value="Binary mask">
-                    </when>
-                </conditional>
-            </repeat>
-        </xml>
+        <import>starting_modules_images.xml</import>
+        <import>starting_modules_metadata.xml</import>
+        <import>starting_modules_nameandtypes.xml</import>
+        <import>starting_modules_groups.xml</import>
     </macros>
+
     <expand macro="py_requirements"/>
 
     <command detect_errors="aggressive"><![CDATA[
-        python '$script_file' '$inputs'
+        python '$__tool_directory__/starting_modules.py' '$inputs'
     ]]></command>
 
     <configfiles>
         <inputs name="inputs"/>
-        <configfile name="script_file">
-import json
-import sys
-import os
-
-FOURSPACES = @SPACES@
-
-input_json_path = sys.argv[1]
-
-params = json.load(open(input_json_path, "r"))
-
-
-def write_images():
-    filter_images = params['images']['filter_images']
-
-    _str = "\nImages:[module_num:1|svn_version:\\'Unknown\\'|variable_revision_number:2|show_window:False|notes:\\x5B\\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]\n"
-    _str += FOURSPACES+":\n"
-    _str += FOURSPACES + "Filter images?:%s\n" % filter_images
-    _str += FOURSPACES + "Select the rule criteria:and (extension does isimage) (directory doesnot startwith \".\")\n"
-
-    return _str
-
-
-def write_metadata():
-    metadata_extraction = params['metadata']['con_metadata_extraction']
-    extract = metadata_extraction['extract']
-
-    if 'extraction_method' in metadata_extraction:
-        method_count = len(metadata_extraction['extraction_method'])
-    else:
-        method_count = 1
-
-    _str = "\nMetadata:[module_num:2|svn_version:\\'Unknown\\'|variable_revision_number:4|show_window:False|notes:\\x5B\\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]\n"
-    _str += FOURSPACES + "Extract metadata?:%s\n" % extract
-
-    if extract == "No":
-        _str += FOURSPACES + "Metadata data type:Text\n"
-        _str += FOURSPACES + "Metadata types:{}\n"
-        _str += FOURSPACES + "Extraction method count:%d\n" % method_count
-        _str += FOURSPACES + "Metadata extraction method:Extract from file/folder names\n"
-        _str += FOURSPACES + "Regular expression to extract from file name:^(?P&lt;Plate>.*)_(?P&lt;Well>\x5BA-P\x5D\x5B0-9\x5D{2})_s(?P&lt;Site>\x5B0-9\x5D)_w(?P&lt;ChannelNumber>\x5B0-9\x5D)\n"
-        _str += FOURSPACES + "Regular expression to extract from folder name:(?P&lt;Date>\x5B0-9\x5D{4}_\x5B0-9\x5D{2}_\x5B0-9\x5D{2})$\n"
-        _str += FOURSPACES + "Extract metadata from:All images\n"
-        _str += FOURSPACES + "Select the filtering criteria:and (file does contain \"\")\n"
-        _str += FOURSPACES + "Metadata file location:\n"
-        _str += FOURSPACES + "Match file and image metadata:\x5B\x5D\n"
-        _str += FOURSPACES + "Use case insensitive matching?:No\n"
-    else:
-        _str += FOURSPACES + "Metadata data type:%s\n" % metadata_extraction['metadata_type']
-        _str += FOURSPACES + "Metadata types:{}\n"
-        _str += FOURSPACES + "Extraction method count:%d\n" % method_count
-
-        for methods in metadata_extraction["extraction_method"]:
-            _str += FOURSPACES + "Metadata extraction method:%s\n" % methods["metadata_extraction_method"]
-            _str += FOURSPACES + "Metadata source:%s\n" % methods["metadata_source"]
-            _str += FOURSPACES + "Regular expression to extract from file name:%s\n" % methods["file_name_regex"]
-            _str += FOURSPACES + "Regular expression to extract from folder name:%s\n" % methods["folder_name_regex"]
-            _str += FOURSPACES + "Extract metadata from:%s\n" % methods["extract_metadata_from"]
-            _str += FOURSPACES + "Select the filtering criteria:and (file does contain \"\")\n"
-            _str += FOURSPACES + "Metadata file location:\n"
-            _str += FOURSPACES + "Match file and image metadata:\x5B\x5D\n"
-            _str += FOURSPACES + "Use case insensitive matching?:No\n"
-
-    return _str
-
-
-def write_nameandtypes():
-    nameandtypes = params['nameandtypes']
-    assign_a_name = nameandtypes['con_assign_a_name_to']['assign_a_name_to']
-
-    if "con_select_image_type" in nameandtypes['con_assign_a_name_to']:
-        con_set_intensity = nameandtypes['con_assign_a_name_to']['con_select_image_type']['con_set_intensity']
-        max_intensity = con_set_intensity['maximum_intensity'] if "maximum_intensity" in con_set_intensity else 255.0
-    else:
-        max_intensity = 255.0
-
-    pixel_space = nameandtypes['pixel_space']
-
-    rule_count = len(nameandtypes['r_match_rule']) if "r_match_rule" in nameandtypes else 1
-
-    process_3d = nameandtypes['pixel_space']['process_3d']
-    x_spacing = 1.0 if "x_spacing" not in pixel_space else pixel_space["x_spacing"]
-    y_spacing = 1.0 if "y_spacing" not in pixel_space else pixel_space["y_spacing"]
-    z_spacing = 1.0 if "z_spacing" not in pixel_space else pixel_space["z_spacing"]
-
-    _str = "\nNamesAndTypes:[module_num:3|svn_version:\\'Unknown\\'|variable_revision_number:8|show_window:False|notes:\\x5B\\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\\'\\x5D|batch_state:array(\\x5B\\x5D, dtype=uint8)|enabled:True|wants_pause:False]\n"
-
-    _str += FOURSPACES + "Assign a name to:%s\n" % assign_a_name
+    </configfiles>
 
-    if assign_a_name == "All images":
-        _str += FOURSPACES + "Select the image type:%s\n" % nameandtypes['con_assign_a_name_to']['con_select_image_type']['select_image_type']
-        _str += FOURSPACES + "Name to assign these images:%s\n" % nameandtypes['con_assign_a_name_to']['name_to_assign']
-        _str += FOURSPACES + "Match metadata:[]\n"
-
-        _str += FOURSPACES + "Image set matching method:Order\n"
-        _str += FOURSPACES + "Set intensity range from:%s\n" % con_set_intensity['set_intensity_range_from']
-        _str += FOURSPACES + "Assignments count:%s\n" % rule_count
-        _str += FOURSPACES + "Single images count:0\n"
-        _str += FOURSPACES + "Maximum intensity:%.1f\n" % max_intensity
-        _str += FOURSPACES + "Process as 3D?:%s\n" % process_3d
-
-        _str += FOURSPACES + "Relative pixel spacing in X:%.1f\n" % x_spacing
-        _str += FOURSPACES + "Relative pixel spacing in Y:%.1f\n" % y_spacing
-        _str += FOURSPACES + "Relative pixel spacing in Z:%.1f\n" % z_spacing
-    else:
-        _str += FOURSPACES + "Select the image type:Grayscale image\n"
-        _str += FOURSPACES + "Name to assign these images:DNA\n"
-        _str += FOURSPACES + "Match metadata:[]\n"
-
-        _str += FOURSPACES + "Image set matching method:%s\n" % nameandtypes['con_assign_a_name_to']['matching_method']
-        _str += FOURSPACES + "Set intensity range from:Image metadata\n"
-        _str += FOURSPACES + "Assignments count:%d\n" % rule_count
-        _str += FOURSPACES + "Single images count:0\n"
-        _str += FOURSPACES + "Maximum intensity:%.1f\n" % max_intensity
-        _str += FOURSPACES + "Process as 3D?:%s\n" % process_3d
-
-        _str += FOURSPACES + "Relative pixel spacing in X:1.0\n"
-        _str += FOURSPACES + "Relative pixel spacing in Y:1.0\n"
-        _str += FOURSPACES + "Relative pixel spacing in Z:1.0\n"
-
-        for rule in nameandtypes["con_assign_a_name_to"]["r_match_rule"]:
-            _str += FOURSPACES + "Select the rule criteria:%s%s%s%s%s%s%s%s%s%s\n" % (rule["match_all_any"], " (",rule["con_match"]["rule_type"], " ",rule["con_match"]["operator"]," ",rule["con_match"]["contain"]," \"",rule["con_match"]["match_value"],"\")")
-            _str += FOURSPACES + "Name to assign these images:%s\n" % rule["name_to_assign"]
-            _str += FOURSPACES + "Name to assign these objects:Cell\n"
-            _str += FOURSPACES + "Select the image type:%s\n" % rule["con_select_image_type"]["select_image_type"]
-
-            intensity_range = rule["con_select_image_type"]["con_set_intensity"]["set_intensity_range_from"]
-
-            _str += FOURSPACES + "Set intensity range from:%s\n" % intensity_range
-            _str += FOURSPACES + "Select the image type:%s\n" % rule["con_select_image_type"]["select_image_type"]
-
-            if intensity_range == "Manual":
-                _str += FOURSPACES + "Maximum intensity:%s\n" % rule["con_select_image_type"]["con_set_intensity"]["maximum_intensity"]
-            else:
-                _str += FOURSPACES + "Maximum intensity:255.0\n"
-
-            if process_3d == "Yes":
-                _str += FOURSPACES + "Relative pixel spacing in X:%.1f\n" % x_spacing
-                _str += FOURSPACES + "Relative pixel spacing in Y:%.1f\n" % y_spacing
-                _str += FOURSPACES + "Relative pixel spacing in Z:%.1f\n" % z_spacing
-
-    return _str
-
-
-def write_groups():
-    groups = params['groups']
-
-    _str = "\nGroups:[module_num:4|svn_version:\\'Unknown\\'|variable_revision_number:2|show_window:False|notes:\\x5B\\\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\\'\\x5D|batch_state:array(\\x5B\\x5D, dtype=uint8)|enabled:True|wants_pause:False]\n"
-
-    _str += FOURSPACES + "Do you want to group your images?:%s\n" % groups["con_groups"]["group_images"]
-    _str += FOURSPACES + "grouping metadata count:1\n"
-    _str += FOURSPACES + "Metadata category:%s\n" % groups["con_groups"]["group_category"]
-
-    return _str
-
-
-with open("output", "w") as f:
-    headers = ["CellProfiler Pipeline: http://www.cellprofiler.org\n",
-               "Version:3\n",
-               "DateRevision:319\n",
-               "GitHash:\n",
-               "ModuleCount:4\n",
-               "HasImagePlaneDetails:False",
-               "\n"]
-
-    f.writelines(headers)
-
-    img_str = write_images()
-    metadata_str = write_metadata()
-    nameandtypes_str = write_nameandtypes()
-    groups_str = write_groups()
-
-    output_str = img_str + metadata_str + nameandtypes_str + groups_str
-
-    f.write(output_str)
-f.close()
-
-        </configfile>
-    </configfiles>
     <inputs>    
         <!-- Images module-->
-        <section name="images" title="Images" expanded="false">
-            <param name="filter_images" type="select" label="Filter images?">
-              <option value="Images only">Images only</option>
-              <option value="No filtering">No filtering</option>
-            </param>
-        </section>
+        <expand macro="starting_modules_images" />
         <!-- Metadata module-->
-        <section name="metadata" title="Metadata" expanded="false">
-            <conditional name="con_metadata_extraction">
-                <param name="extract" type="select" display="radio" label="Extract metadata?">
-                    <option value="No">No</option>
-                    <option value="Yes">Yes</option>
-                </param>
-                <when value="Yes">
-                    <repeat name="extraction_method" title="metadata">
-                        <param name="metadata_extraction_method" type="select" label="Metadata extraction method">
-                            <option value="Extract from file/folder names">Extract from file/folder names</option>
-                            <option value="Import from file">Import from file</option>
-                            <option value="Extract from image file headers">Extract from image file headers</option>
-                        </param>
-                        <param name="metadata_source" type="select" label="Metadata source">
-                            <option value="File name">File name</option>
-                            <option value="Folder name">Folder name</option>
-                        </param>
-                        <param name="file_name_regex" type="select" label="Select file name pattern to extract from file name" help="Image file names must comply with one of the patterns.For example, AS_09125_050116030001_D03f00d0.tif matches the pattern field1_filed2_field3_field4. If none of the patterns are suitable, please use other Galaxy tools to rename your files first.  ">
-                            <sanitizer sanitize="false"/>
-                            <option value="(?P&lt;field1>.*)">field1</option>
-                            <option value="(?P&lt;field1>.*)-(?P&lt;field2>[a-zA-Z0-9]+)">field1-field2</option>
-                            <option value="(?P&lt;field1>.*)_(?P&lt;field2>[a-zA-Z0-9]+)">field1_field2</option>
-                            <option value="(?P&lt;field1>.*)__(?P&lt;field2>[a-zA-Z0-9]+)">field1__field2</option>
-                            <option value="(?P&lt;field1>.*)-(?P&lt;field2>[a-zA-Z0-9]+)-(?P&lt;field3>[a-zA-Z0-9]+)">field1-field2-field3</option>
-                            <option value="(?P&lt;field1>.*)_(?P&lt;field2>[a-zA-Z0-9]+)_(?P&lt;field3>[a-zA-Z0-9]+)">field1_field2_field3</option>
-                            <option value="(?P&lt;field1>.*)__(?P&lt;field2>[a-zA-Z0-9]+)__(?P&lt;field3>[a-zA-Z0-9]+)">field1__field2__field3</option>
-                            <option value="(?P&lt;field1>.*)-(?P&lt;field2>[a-zA-Z0-9]+)-(?P&lt;field3>[a-zA-Z0-9]+)-(?P&lt;field4>[a-zA-Z0-9]+)">field1-field2-field3-field4</option>
-                            <option value="(?P&lt;field1>.*)_(?P&lt;field2>[a-zA-Z0-9]+)_(?P&lt;field3>[a-zA-Z0-9]+)_(?P&lt;field4>[a-zA-Z0-9]+)">field1_field2_field3_field4</option>
-                            <option value="(?P&lt;field1>.*)__(?P&lt;field2>[a-zA-Z0-9]+)__(?P&lt;field3>[a-zA-Z0-9]+)__(?P&lt;field4>[a-zA-Z0-9]+)">field1__field2__field3__field4</option>
-                            <option value="(?P&lt;field1>.*)-(?P&lt;field2>[a-zA-Z0-9]+)-(?P&lt;field3>[a-zA-Z0-9]+)-(?P&lt;field4>[a-zA-Z0-9]+)-(?P&lt;field5>[a-zA-Z0-9]+)">field1-field2-field3-field4-field5</option>
-                            <option value="(?P&lt;field1>.*)_(?P&lt;field2>[a-zA-Z0-9]+)_(?P&lt;field3>[a-zA-Z0-9]+)_(?P&lt;field4>[a-zA-Z0-9]+)_(?P&lt;field5>[a-zA-Z0-9]+)">field1_field2_field3_field4_field5</option>
-                            <option value="(?P&lt;field1>.*)__(?P&lt;field2>[a-zA-Z0-9]+)__(?P&lt;field3>[a-zA-Z0-9]+)__(?P&lt;field4>[a-zA-Z0-9]+)__(?P&lt;field5>[a-zA-Z0-9]+)">field1__field2__field3__field4__field5</option>
-                            <option value="(?P&lt;field1>.*)-(?P&lt;field2>[a-zA-Z0-9]+)-(?P&lt;field3>[a-zA-Z0-9]+)-(?P&lt;field4>[a-zA-Z0-9]+)-(?P&lt;field5>[a-zA-Z0-9]+)-(?P&lt;field6>[a-zA-Z0-9]+)">field1-field2-field3-field4-field5-field6</option>
-                            <option value="(?P&lt;field1>.*)_(?P&lt;field2>[a-zA-Z0-9]+)_(?P&lt;field3>[a-zA-Z0-9]+)_(?P&lt;field4>[a-zA-Z0-9]+)_(?P&lt;field5>[a-zA-Z0-9]+)_(?P&lt;field6>[a-zA-Z0-9]+)">field1_field2_field3_field4_field5_field6</option>
-                            <option value="(?P&lt;field1>.*)__(?P&lt;field2>[a-zA-Z0-9]+)__(?P&lt;field3>[a-zA-Z0-9]+)__(?P&lt;field4>[a-zA-Z0-9]+)__(?P&lt;field5>[a-zA-Z0-9]+)__(?P&lt;field6>[a-zA-Z0-9]+)">field1__field2__field3__field4__field5__field6</option>
-                        </param>
-                        <param name="folder_name_regex" type="select" label="Select folder name pattern to extract from folder name" help="Folder names must comply with one of the patterns.For example, folder name images-exp1 matches the pattern field1-field2. If none of the patterns are suitable, please use other Galaxy tools to rename your folder first.  "> 
-                            <sanitizer sanitize="false"/>
-                            <option value="(?P&lt;field1>.*)">field1</option>
-                            <option value="(?P&lt;field1>.*)-(?P&lt;field2>[a-zA-Z0-9]+)">field1-field2</option>
-                            <option value="(?P&lt;field1>.*)_(?P&lt;field2>[a-zA-Z0-9]+)">field1_field2</option>
-                        </param>
-                        <param name="extract_metadata_from" type="select" label="Extract metadata from">
-                            <option value="All images">All images</option>
-                            <option value="Images matching a rule">Images matching a rule</option>
-                        </param>
-                    </repeat>
-                    <param name="metadata_type" type="select" label="Metadata data type">      
-                        <option value="Text">Text</option>
-                    </param>
-                </when>
-                <when value="No">
-                </when>
-            </conditional>
-        </section>
+        <expand macro="starting_modules_metadata" />
         <!-- NamesAndTypes-->
-        <section name="nameandtypes" title="NamesAndTypes" expanded="false">
-            <conditional name="pixel_space">
-                <param name="process_3d" type="select" display="radio" label="Process 3D">
-                    <option value="No">No</option>
-                    <option value="Yes">Yes</option>
-                </param>  
-                <when value="Yes">
-                    <param name="x_spacing" type="float" value="1.0" label="Relative pixel spacing in X"/>
-                    <param name="y_spacing" type="float" value="1.0" label="Relative pixel spacing in Y"/>
-                    <param name="z_spacing" type="float" value="1.0" label="Relative pixel spacing in Z"/>
-                </when>
-                <when value="No">
-                </when>
-            </conditional>
-            <conditional name="con_assign_a_name_to">
-                <param name="assign_a_name_to" type="select" label="Assign a name to">
-                    <option value="All images">All images</option>
-                    <option value="Images matching rules">Images matching rules</option>
-                </param>
-                <when value="All images">
-                    <param name="name_to_assign" type="text" value="DNA" label="Name to assign these images"/>
-                    <conditional name="con_select_image_type">
-                        <param name="select_image_type" type="select" label="Select the image type">
-                            <option value="Grayscale image">Grayscale image</option>
-                            <option value="Color image">Color image</option>
-                            <option value="Binary mask">Binary mask</option>
-                        </param>
-                        <when value ="Grayscale image">
-                            <expand macro="image_type_condition" />
-                        </when>
-                        <when value="Color image">
-                            <expand macro="image_type_condition" />
-                        </when>
-                        <when value="Binary mask">
-                        </when>
-                    </conditional>
-                </when>
-                <when value="Images matching rules">
-                    <expand macro="image_matching_rules"/>
-                    <param name="matching_method" type="select" label="Image set matching method">
-                        <option value="Order">Order</option>
-                        <option value="Metadata">Metadata</option>
-                    </param>
-                </when>
-            </conditional>
-        </section>
+        <expand macro="starting_modules_nameandtypes" />
         <!-- Groups -->
-        <section name="groups" title="Groups" expanded="false">
-            <conditional name="con_groups">
-                <param name="group_images" type="select" value="No" label="Do you want to group your images?" display="radio">
-                    <option value="Yes">Yes</option>
-                    <option value="No">No</option>
-                </param>
-                <when value="Yes">
-                    <param name="group_category" type="select" label="Metadata category">
-                        <option value="FileLocation">FileLocation</option>
-                        <option value="Frame">Frame</option>
-                        <option value="ImageId">ImageId</option>
-                        <option value="Screen">Screen</option>
-                        <option value="Series">Series</option>
-                        <option value="field1">field1</option>
-                        <option value="field2">field2</option>
-                        <option value="field3">field3</option>
-                        <option value="field4">field4</option>
-                        <option value="field5">field5</option>
-                        <option value="field6">field6</option>
-                    </param>
-                </when>
-                <when value="No">
-                </when>
-            </conditional>
-        </section>
+        <expand macro="starting_modules_groups" />
     </inputs>
     <outputs>
-        <expand macro="output_pipeline_macro" />
+        <expand macro="output_pipeline_param" />
     </outputs>
     <tests>
         <test>
+            <!-- one big test case for various inputs scenarios -->
             <param name="filter_images" value="Images only"/>
             <conditional name="con_metadata_extraction">
                 <param name="extract" value="Yes"/>
                 <repeat name="extraction_method">
                     <param name="metadata_extraction_method" value="Extract from file/folder names"/>
-                    <param name="metadata_source" value="File name" />
-                    <param name="file_name_regex" value="(?P&lt;field1>.*)_(?P&lt;field2>[a-zA-Z0-9]+)_(?P&lt;field3>[a-zA-Z0-9]+)_(?P&lt;field4>[a-zA-Z0-9]+)" />
-                    <param name="extract_metadata_from" value="All images" />
+                    <conditional name="con_metadata_extract_from">
+                        <param name="match_all_any" value="and" />
+                        <repeat name="r_match">
+                            <conditional name="con_match">
+                                <param name="operator" value="does"/>
+                                <param name="rule_type" value="file"/>
+                                <param name="match_value" value="im"/>
+                                <param name="contain" value="contain"/>
+                            </conditional>
+                        </repeat>
+                        <repeat name="r_match">
+                            <conditional name="con_match">
+                                <param name="operator" value="does"/>
+                                <param name="rule_type" value="extension"/>
+                                <param name="match_type" value="istif"/>
+                            </conditional>
+                        </repeat>
+                        <param name="extract_metadata_from" value="Images matching a rule" />
+                    </conditional>
+                    <conditional name="con_metadata_source">
+                        <param name="metadata_source" value="File name" />
+                        <param name="file_name_regex" value="(?P&lt;field1>.*)_(?P&lt;field2>[a-zA-Z0-9]+)_(?P&lt;field3>[a-zA-Z0-9]+)_(?P&lt;field4>[a-zA-Z0-9]+)" />
+                    </conditional>
                 </repeat>
-                <param name="metadata_type" value="Text" />
+                <repeat name="extraction_method">
+                    <param name="metadata_extraction_method" value="Extract from file/folder names"/>
+                    <conditional name="con_metadata_extract_from">
+                        <param name="extract_metadata_from" value="All images" />
+                    </conditional>
+                    <conditional name="con_metadata_source">
+                        <param name="metadata_source" value="Folder name" />
+                        <param name="folder_name_regex" value="(?P&lt;folderField1>.*)_(?P&lt;folderField2>[a-zA-Z0-9]+)" />
+                    </conditional>
+                </repeat>
             </conditional>
             <conditional name="pixel_space">
                 <param name="process_3d" value="No"/>
@@ -421,14 +81,47 @@
                 <param name="assign_a_name_to" value="Images matching rules"/>
                 <repeat name="r_match_rule">
                     <param name="match_all_any" value="and" />
-                    <conditional name="con_match">
-                        <param name="rule_type" value="file" />
-                        <param name="operator" value="does" />
-                        <param name="contain" value="startwith" />
-                        <param name="match_value" value="im" /> 
+                    <repeat name="r_match">
+                        <conditional name="con_match">
+                            <param name="rule_type" value="file" />
+                            <param name="operator" value="does" />
+                            <param name="contain" value="contain" />
+                            <param name="match_value" value="im" />
+                        </conditional>
+                    </repeat>
+                    <repeat name="r_match">
+                        <conditional name="con_match">
+                            <param name="rule_type" value="image" />
+                            <param name="operator" value="doesnot" />
+                            <param name="match_type" value="ismonochrome" />
+                        </conditional>
+                    </repeat>
+                    <conditional name="con_select_image_type">
+                        <param name="name_to_assign" value="Cell" />
+                        <param name="select_image_type" value="Objects" />
                     </conditional>
-                    <param name="name_to_assign" value="DNA" />
+                </repeat>
+
+                <repeat name="r_match_rule">
+                    <param name="match_all_any" value="and" />
+                    <repeat name="r_match" />
                     <conditional name="con_select_image_type">
+                        <param name="name_to_assign" value="GFP" />
+                        <param name="select_image_type" value="Illumination function" />
+                    </conditional>
+                </repeat>
+
+                <repeat name="r_match_rule">
+                    <param name="match_all_any" value="or" />
+                    <repeat name="r_match">
+                        <conditional name="con_match">
+                            <param name="rule_type" value="extension" />
+                            <param name="operator" value="does" />
+                            <param name="match_type" value="istif" />
+                        </conditional>
+                    </repeat>
+                    <conditional name="con_select_image_type">
+                        <param name="name_to_assign" value="Actin" />
                         <param name="select_image_type" value="Grayscale image" />
                         <conditional name="con_set_intensity">
                             <param name="set_intensity_range_from" value="Image metadata" />
@@ -439,26 +132,151 @@
             </conditional>
             <conditional name="con_groups">
                 <param name="group_images" value="Yes" />
-                <param name="group_category" value="Screen" />
+                <param name="group_category" value="field1" />
+            </conditional>
+            <expand macro="test_out_file" file="common-complicated.cppipe"/>
+        </test>
+        <test>
+            <!-- Repeat test for no grouping -->
+            <param name="filter_images" value="Images only"/>
+            <conditional name="con_metadata_extraction">
+                <param name="extract" value="Yes"/>
+                <repeat name="extraction_method">
+                    <param name="metadata_extraction_method" value="Extract from file/folder names"/>
+                    <conditional name="con_metadata_extract_from">
+                        <param name="match_all_any" value="and" />
+                        <repeat name="r_match">
+                            <conditional name="con_match">
+                                <param name="operator" value="does"/>
+                                <param name="rule_type" value="file"/>
+                                <param name="match_value" value="im"/>
+                                <param name="contain" value="contain"/>
+                            </conditional>
+                        </repeat>
+                        <repeat name="r_match">
+                            <conditional name="con_match">
+                                <param name="operator" value="does"/>
+                                <param name="rule_type" value="extension"/>
+                                <param name="match_type" value="istif"/>
+                            </conditional>
+                        </repeat>
+                        <param name="extract_metadata_from" value="Images matching a rule" />
+                    </conditional>
+                    <conditional name="con_metadata_source">
+                        <param name="metadata_source" value="File name" />
+                        <param name="file_name_regex" value="(?P&lt;field1>.*)_(?P&lt;field2>[a-zA-Z0-9]+)_(?P&lt;field3>[a-zA-Z0-9]+)_(?P&lt;field4>[a-zA-Z0-9]+)" />
+                    </conditional>
+                </repeat>
+                <repeat name="extraction_method">
+                    <param name="metadata_extraction_method" value="Extract from file/folder names"/>
+                    <conditional name="con_metadata_extract_from">
+                        <param name="extract_metadata_from" value="All images" />
+                    </conditional>
+                    <conditional name="con_metadata_source">
+                        <param name="metadata_source" value="Folder name" />
+                        <param name="folder_name_regex" value="(?P&lt;folderField1>.*)_(?P&lt;folderField2>[a-zA-Z0-9]+)" />
+                    </conditional>
+                </repeat>
+            </conditional>
+            <conditional name="pixel_space">
+                <param name="process_3d" value="No"/>
             </conditional>
-            <expand macro="test_out_file" />
+            <conditional name="con_assign_a_name_to">
+                <param name="assign_a_name_to" value="Images matching rules"/>
+                <repeat name="r_match_rule">
+                    <param name="match_all_any" value="and" />
+                    <repeat name="r_match">
+                        <conditional name="con_match">
+                            <param name="rule_type" value="file" />
+                            <param name="operator" value="does" />
+                            <param name="contain" value="contain" />
+                            <param name="match_value" value="im" />
+                        </conditional>
+                    </repeat>
+                    <repeat name="r_match">
+                        <conditional name="con_match">
+                            <param name="rule_type" value="image" />
+                            <param name="operator" value="doesnot" />
+                            <param name="match_type" value="ismonochrome" />
+                        </conditional>
+                    </repeat>
+                    <conditional name="con_select_image_type">
+                        <param name="name_to_assign" value="Cell" />
+                        <param name="select_image_type" value="Objects" />
+                    </conditional>
+                </repeat>
+
+                <repeat name="r_match_rule">
+                    <param name="match_all_any" value="and" />
+                    <repeat name="r_match" />
+                    <conditional name="con_select_image_type">
+                        <param name="name_to_assign" value="GFP" />
+                        <param name="select_image_type" value="Illumination function" />
+                    </conditional>
+                </repeat>
+
+                <repeat name="r_match_rule">
+                    <param name="match_all_any" value="or" />
+                    <repeat name="r_match">
+                        <conditional name="con_match">
+                            <param name="rule_type" value="extension" />
+                            <param name="operator" value="does" />
+                            <param name="match_type" value="istif" />
+                        </conditional>
+                    </repeat>
+                    <conditional name="con_select_image_type">
+                        <param name="name_to_assign" value="Actin" />
+                        <param name="select_image_type" value="Grayscale image" />
+                        <conditional name="con_set_intensity">
+                            <param name="set_intensity_range_from" value="Image metadata" />
+                        </conditional>
+                    </conditional>
+                </repeat>
+                <param name="matching_method" value="Order" />
+            </conditional>
+            <conditional name="con_groups">
+                <param name="group_images" value="No" />
+            </conditional>
+            <expand macro="test_out_file" file="common-nogroup.cppipe" />
         </test>
     </tests>
 
     <help>
-    This tool builds a CellProfiler pipeline file with headers and 4 compulsory modules, 'Images', 'Metadata', 'NamesAndTypes' and 'Groups'.
+        <![CDATA[
+
+        .. class:: infomark
+
+        **What it does**
+
+        This tool is the first in a CellProfiler pipeline and includes the first four modules:
 
-    No input parameters are needed for this tool. The rest CP modules will build based on the output of this file.
+        *Images*: use the Images module to compile a list of files that you want to analyze. 
+
+        *Metadata*: optionally allows you to extract information describing your images (i.e., metadata) which will be stored along with your measurements. 
 
- 
-    Images: use the Images module to compile a list of files that you want to analyze. 
+        *NamesAndTypes*: allows you to assign a meaningful name to each image by which other modules will refer to it.
+
+        *Groups*: optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.
+
+        .. class:: infomark
 
-    Metadata: optionally allows you to extract information describing your images (i.e., metadata) which will be stored along with your measurements. 
+        **Input**
+
+        No input parameters are needed for this tool. 
+
+        .. class:: infomark
+
+        **Output**
 
-    NamesAndTypes: allows you to assign a meaningful name to each image by which other modules will refer to it.
+        A CellProfiler pipeline file *(.cppipe)* with the settings of the 4 modules.
+
+        .. class:: warningmark
 
-    Groups: optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.
+        **IMPORTANT**
 
+        This tool has to be the first one in a CellProfiler workflow and the last one **CellProfiler**.
+
+        ]]>    
     </help>
     <expand macro="citations" />
 </tool>
diff -r 3c3cd68d6d5a -r 27396311a314 starting_modules_groups.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/starting_modules_groups.xml	Mon May 11 07:45:07 2020 -0400
@@ -0,0 +1,32 @@
+<macros>
+    <xml name="starting_modules_groups">
+        <section name="groups" title="Groups" expanded="false">
+        <conditional name="con_groups">
+            <param name="group_images" type="select" value="No" label="Do you want to group your images?">
+                <option value="Yes">Yes, group the images</option>
+                <option value="No" selected="true">No, do not group images</option>
+            </param>
+            <when value="Yes">
+                <param name="group_category" type="select" label="Metadata category">
+                    <option value="None" selected="true">None</option>
+                    <option value="ChannelNumber">Channel number</option>
+                    <option value="FileLocation">File location</option>
+                    <option value="Plate">Plate</option>
+                    <option value="Frame">Frame</option>
+                    <option value="Series">Series</option>
+                    <option value="Site">Site</option>
+                    <option value="Well">Well</option>
+                    <option value="field1">field1</option>
+                    <option value="field2">field2</option>
+                    <option value="field3">field3</option>
+                    <option value="field4">field4</option>
+                    <option value="field5">field5</option>
+                    <option value="field6">field6</option>
+                </param>
+            </when>
+            <when value="No">
+            </when>
+        </conditional>
+    </section>
+    </xml>
+</macros>
\ No newline at end of file
diff -r 3c3cd68d6d5a -r 27396311a314 starting_modules_image.xml
diff -r 3c3cd68d6d5a -r 27396311a314 starting_modules_images.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/starting_modules_images.xml	Mon May 11 07:45:07 2020 -0400
@@ -0,0 +1,10 @@
+<macros>
+    <xml name="starting_modules_images">
+        <section name="images" title="Images" expanded="false">
+            <param name="filter_images" type="select" label="Do you want to filter only the images?" help="Enabling file filtering is useful if, for example, you drag-and-dropped a folder onto the file list panel which contains a mixture of images that you want to analyze and other files that you want to ignore.">
+                <option value="Images only">Select the images only</option>
+                <option value="No filtering">Select all the files</option>
+            </param>
+        </section>
+    </xml>
+</macros>
\ No newline at end of file
diff -r 3c3cd68d6d5a -r 27396311a314 starting_modules_metadata.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/starting_modules_metadata.xml	Mon May 11 07:45:07 2020 -0400
@@ -0,0 +1,92 @@
+<macros>
+    <xml name="image_matching_rules_metadata">
+        <param name="match_all_any" type="select" display="radio" label="Match the following rules">
+            <option value="and">All</option>
+            <option value="or">Any</option>
+        </param>
+        <repeat name="r_match" title="filtering rules">
+            <conditional name="con_match">
+                <param name="rule_type" type="select" label="Select the filtering criteria">
+                    <option value="file">File</option>
+                    <option value="directory">Directory</option>
+                    <option value="extension">Extension</option>
+                </param>
+                <when value="file">
+                    <expand macro="name_type_rule_matching_file"/>
+                </when>
+                <when value="directory">
+                    <expand macro="name_type_rule_matching_file"/>
+                </when>
+                <when value="extension">
+                    <expand macro="name_type_rule_ext" />
+                </when>
+            </conditional>
+        </repeat>
+    </xml>
+    <xml name="starting_modules_metadata">
+        <section name="metadata" title="Metadata" expanded="false">
+            <conditional name="con_metadata_extraction">
+                <param name="extract" type="select" label="Do you want to extract the metadata?">
+                    <option value="Yes">Yes, specify metadata</option>
+                    <option value="No" selected="true">No, do not specify metadata</option>
+                </param>
+                <when value="Yes">
+                    <repeat name="extraction_method" title="new metadata" min="1">
+                        <param name="metadata_extraction_method" type="select" label="Metadata extraction method" help="Metadata can be stored in either or both of two ways: internally (through the file naming, directory structuring, or the file header information) or externally (external index, such as spreadsheet or database of some kind). " >
+                            <option value="Extract from file/folder names">Extract from file/folder names</option>
+                            <option value="Import from file">Import from file</option>
+                            <option value="Extract from image file headers">Extract from image file headers</option>
+                        </param>
+                        <conditional name="con_metadata_source">
+                            <param name="metadata_source" type="select" label="Metadata source" help="You can extract the metadata from the image file name or from its folder name.">
+                                <option value="File name">File name</option>
+                                <option value="Folder name">Folder name</option>
+                            </param>
+                            <when value="File name">
+                                <param name="file_name_regex" type="select" label="Select the pattern to extract metadata from the file name" help="Image file names must comply with one of the patterns. For example, plate_reagent_timepoint.tif matches the pattern field1_field2_field3. If none of the patterns is suitable, please use other Galaxy tools to rename your files first.">
+
+                                    <sanitizer sanitize="false"/>
+                                    <option value="(?P&lt;field1>.*)">field1</option>
+                                    <option value="(?P&lt;field1>.*)-(?P&lt;field2>[a-zA-Z0-9]+)">field1-field2</option>
+                                    <option value="(?P&lt;field1>.*)_(?P&lt;field2>[a-zA-Z0-9]+)">field1_field2</option>
+                                    <option value="(?P&lt;field1>.*)__(?P&lt;field2>[a-zA-Z0-9]+)">field1__field2</option>
+                                    <option value="(?P&lt;field1>.*)-(?P&lt;field2>[a-zA-Z0-9]+)-(?P&lt;field3>[a-zA-Z0-9]+)">field1-field2-field3</option>
+                                    <option value="(?P&lt;field1>.*)_(?P&lt;field2>[a-zA-Z0-9]+)_(?P&lt;field3>[a-zA-Z0-9]+)">field1_field2_field3</option>
+                                    <option value="(?P&lt;field1>.*)__(?P&lt;field2>[a-zA-Z0-9]+)__(?P&lt;field3>[a-zA-Z0-9]+)">field1__field2__field3</option>
+                                    <option value="(?P&lt;field1>.*)-(?P&lt;field2>[a-zA-Z0-9]+)-(?P&lt;field3>[a-zA-Z0-9]+)-(?P&lt;field4>[a-zA-Z0-9]+)">field1-field2-field3-field4</option>
+                                    <option value="(?P&lt;field1>.*)_(?P&lt;field2>[a-zA-Z0-9]+)_(?P&lt;field3>[a-zA-Z0-9]+)_(?P&lt;field4>[a-zA-Z0-9]+)">field1_field2_field3_field4</option>
+                                    <option value="(?P&lt;field1>.*)__(?P&lt;field2>[a-zA-Z0-9]+)__(?P&lt;field3>[a-zA-Z0-9]+)__(?P&lt;field4>[a-zA-Z0-9]+)">field1__field2__field3__field4</option>
+                                    <option value="(?P&lt;field1>.*)-(?P&lt;field2>[a-zA-Z0-9]+)-(?P&lt;field3>[a-zA-Z0-9]+)-(?P&lt;field4>[a-zA-Z0-9]+)-(?P&lt;field5>[a-zA-Z0-9]+)">field1-field2-field3-field4-field5</option>
+                                    <option value="(?P&lt;field1>.*)_(?P&lt;field2>[a-zA-Z0-9]+)_(?P&lt;field3>[a-zA-Z0-9]+)_(?P&lt;field4>[a-zA-Z0-9]+)_(?P&lt;field5>[a-zA-Z0-9]+)">field1_field2_field3_field4_field5</option>
+                                    <option value="(?P&lt;field1>.*)__(?P&lt;field2>[a-zA-Z0-9]+)__(?P&lt;field3>[a-zA-Z0-9]+)__(?P&lt;field4>[a-zA-Z0-9]+)__(?P&lt;field5>[a-zA-Z0-9]+)">field1__field2__field3__field4__field5</option>
+                                    <option value="(?P&lt;field1>.*)-(?P&lt;field2>[a-zA-Z0-9]+)-(?P&lt;field3>[a-zA-Z0-9]+)-(?P&lt;field4>[a-zA-Z0-9]+)-(?P&lt;field5>[a-zA-Z0-9]+)-(?P&lt;field6>[a-zA-Z0-9]+)">field1-field2-field3-field4-field5-field6</option>
+                                    <option value="(?P&lt;field1>.*)_(?P&lt;field2>[a-zA-Z0-9]+)_(?P&lt;field3>[a-zA-Z0-9]+)_(?P&lt;field4>[a-zA-Z0-9]+)_(?P&lt;field5>[a-zA-Z0-9]+)_(?P&lt;field6>[a-zA-Z0-9]+)">field1_field2_field3_field4_field5_field6</option>
+                                    <option value="(?P&lt;field1>.*)__(?P&lt;field2>[a-zA-Z0-9]+)__(?P&lt;field3>[a-zA-Z0-9]+)__(?P&lt;field4>[a-zA-Z0-9]+)__(?P&lt;field5>[a-zA-Z0-9]+)__(?P&lt;field6>[a-zA-Z0-9]+)">field1__field2__field3__field4__field5__field6</option>
+                                </param>
+                            </when>
+                            <when value="Folder name">
+                                <param name="folder_name_regex" type="select" label="Select the pattern to extract metadata from the folder name" help="Folder names must comply with one of the patterns. For example, folder name exp1-channel_name matches the pattern field1-field2. If none of the patterns is suitable, please use other Galaxy tools to rename your folder first.">
+                                    <sanitizer sanitize="false"/>
+                                    <option value="(?P&lt;folderField1>.*)">field1</option>
+                                    <option value="(?P&lt;folderField1>.*)-(?P&lt;folderField2>[a-zA-Z0-9]+)">field1-field2</option>
+                                    <option value="(?P&lt;folderField1>.*)_(?P&lt;folderField2>[a-zA-Z0-9]+)">field1_field2</option>
+                                </param>
+                            </when>
+                        </conditional>
+                        <conditional name="con_metadata_extract_from">
+                            <param name="extract_metadata_from" type="select" label="Extract metadata from">
+                                <option value="All images">All images</option>
+                                <option value="Images matching a rule">Images matching a rule</option>
+                            </param>
+                            <when value="Images matching a rule">
+                                <expand macro="image_matching_rules_metadata" />
+                            </when>
+                            <when value="All images" />
+                        </conditional>
+                    </repeat>
+                </when>
+                <when value="No" />
+            </conditional>
+        </section>
+    </xml>
+</macros>
diff -r 3c3cd68d6d5a -r 27396311a314 starting_modules_nameandtypes.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/starting_modules_nameandtypes.xml	Mon May 11 07:45:07 2020 -0400
@@ -0,0 +1,182 @@
+<macros>
+    <xml name="macro_image_type" token_thing="images">
+        <param name="name_to_assign" type="text" value="DNA" label="Name to assign these @THING@" />
+    </xml>
+    
+    <xml name="image_type_condition"> 
+        <conditional name="con_set_intensity">
+            <param name="set_intensity_range_from" type="select" label="Set intensity range from" help="This option determines how the image intensity should be rescaled from 0.0 - 1.0.">
+                <option value="Image metadata">Image metadata</option>
+                <option value="Image bit-depth">Image bit-depth</option>
+                <option value="Manual">Manual</option>
+            </param>
+            <when value="Manual">
+                <param name="maximum_intensity" type="float" value="255.0" label="Maximum intensity" help="The pixel value is divided, as read from the image file, by this value to get the loaded image’s per-pixel intensity." />
+
+            </when>
+            <when value="Image metadata" />
+            <when value="Image bit-depth" />
+        </conditional>
+    </xml>
+    <xml name="name_type_rule_matching_file">
+        <param name="operator" type="select">
+            <option value="does">Does</option>
+            <option value="doesnot">Does not</option>
+        </param>
+        <param name="contain" type="select">
+            <option value="contain">Contain</option>
+            <option value="Contain regular expression">Contain regular expression</option>
+            <option value="startwith">Start with</option>
+            <option value="endwith">End with</option>
+            <option value="Exactly match">Exactly match</option>
+        </param>
+        <param name="match_value" type="text"/>
+    </xml>
+    <xml name="name_type_rule_image">
+        <param name="operator" type="select">
+            <option value="does">Is</option>
+            <option value="doesnot">Is not</option>
+        </param>
+        <param name="match_type" type="select">
+            <option value="iscolor">Color</option>
+            <option value="ismonochrome">Monochrome</option>
+            <option value="isstack">Stack</option>
+            <option value="isstackframe">Stack frame</option>
+        </param>
+    </xml>
+    <xml name="name_type_rule_metadata">
+        <param name="operator" type="select">
+            <option value="does">Does</option>
+            <option value="doesnot">Does not</option>
+        </param>
+        <param name="match_type" type="select">
+            <option value="FileLocation">Have FileLocation matching</option>
+            <option value="Frame">Have Frame matching</option>
+            <option value="Screen">Have Screen matching</option>
+            <option value="Series">Have Series matching</option>
+        </param>
+        <param name="match_value" type="text"/>
+    </xml>
+    <xml name="name_type_rule_ext">
+        <param name="operator" type="select">
+            <option value="does">Is</option>
+            <option value="doesnot">Is not</option>
+        </param>
+        <param name="match_type" type="select">
+            <option value="istif">tif, tiff, ome.tif or ome.tiff</option>
+            <option value="isjpeg">jpg, jpeg</option>
+            <option value="ispng">png</option>
+            <option value="isimage">the extension of an image file</option>
+            <option value="isflex">flex</option>
+            <option value="ismovie">mov, avi</option>
+
+        </param>
+    </xml>
+    <xml name="image_matching_rules">
+        <repeat name="r_match_rule" title="Another image">
+            <param name="match_all_any" type="select" display="radio" label="Match the following rules">
+                <option value="and">All</option>
+                <option value="or">Any</option>
+            </param>
+            <repeat name="r_match" title="rule">
+                <conditional name="con_match">
+                    <param name="rule_type" type="select" label="Select rule criteria">
+                        <option value="file">File</option>
+                        <option value="directory">Directory</option>
+                        <option value="extension">Extension</option>
+                        <option value="image">Image</option>
+                        <option value="metadata">Metadata</option>
+                    </param>
+                    <when value="file">
+                        <expand macro="name_type_rule_matching_file"/>
+                    </when>
+                    <when value="directory">
+                        <expand macro="name_type_rule_matching_file"/>
+                    </when>
+                    <when value="extension">
+                        <expand macro="name_type_rule_ext" />
+                    </when>
+                    <when value="image">
+                        <expand macro="name_type_rule_image" />
+                    </when>
+                    <when value="metadata">
+                        <expand macro="name_type_rule_metadata" />
+                    </when>
+                </conditional>
+            </repeat>
+            <conditional name="con_select_image_type">
+                <param name="select_image_type" type="select" label="Select the image type" help="You can specify how these images should be treated">
+                    <option value="Grayscale image">Grayscale image</option>
+                    <option value="Color image">Color image</option>
+                    <option value="Binary mask">Binary mask</option>
+                    <option value="Illumination function">Illumination function</option>
+                    <option value="Objects">Objects</option>
+
+                </param>
+                <when value ="Grayscale image">
+                    <expand macro="macro_image_type" thing="images"/>
+                    <expand macro="image_type_condition" />
+                </when>
+                <when value="Color image">
+                    <expand macro="macro_image_type" thing="images"/>
+                    <expand macro="image_type_condition" />
+                </when>
+                <when value="Binary mask">
+                    <expand macro="macro_image_type" thing="images"/>
+                </when>
+                <when value="Illumination function">
+                    <expand macro="macro_image_type" thing="images"/>
+                </when>
+                <when value="Objects">
+                    <expand macro="macro_image_type" thing="objects"/>
+                </when>
+            </conditional>
+        </repeat>
+    </xml>
+    <xml name="starting_modules_nameandtypes">
+        <section name="nameandtypes" title="NamesAndTypes" expanded="false">
+            <conditional name="pixel_space">
+                <param name="process_3d" type="select" label="Process 3D" help="If you want to treat the data as three-dimensional, select 'Yes' to load files as volumes. Otherwise, select 'No' to load files as separate, two-dimensional images.">
+                    <option value="Yes">Yes, process 3D data</option>
+                    <option value="No">No, do not process 3D data</option>
+                </param>  
+                <when value="Yes">
+                    <param name="x_spacing" type="float" value="1.0" label="Enter the spacing between voxels in the X dimension, relative to Y and Z" help="Normally, you will set one of these values to 1 and the others relative to that." />
+                    <param name="y_spacing" type="float" value="1.0" label="Enter the spacing between voxels in the Y dimension, relative to X and Z"/>
+                    <param name="z_spacing" type="float" value="1.0" label="Enter the spacing between voxels in the Z dimension, relative to X and Y"/>
+                </when>
+                <when value="No"/>
+            </conditional>
+            <conditional name="con_assign_a_name_to">
+                <param name="assign_a_name_to" type="select" label="Assign a name to" help="This setting allows you to specify a name for types of images or subsets of images so they can be treated separately by downstream tools.">
+                    <option value="All images">Give every image the same name</option>
+                    <option value="Images matching rules">Give images one of several names depending on the metadata</option>
+                </param>
+                <when value="All images">
+                    <expand macro="macro_image_type" thing="images" />
+                    <conditional name="con_select_image_type">
+                        <param name="select_image_type" type="select" label="Select the image type">
+                            <option value="Grayscale image">Grayscale image</option>
+                            <option value="Color image">Color image</option>
+                            <option value="Binary mask">Binary mask</option>
+                        </param>
+                        <when value ="Grayscale image">
+                            <expand macro="image_type_condition" />
+                        </when>
+                        <when value="Color image">
+                            <expand macro="image_type_condition" />
+                        </when>
+                        <when value="Binary mask" />
+                    </conditional>
+                </when>
+            <when value="Images matching rules">
+                <expand macro="image_matching_rules"/>
+                <param name="matching_method" type="select" label="Image set matching method">
+                    <option value="Order">Order</option>
+                    <option value="Metadata">Metadata</option>
+                </param>
+            </when>
+        </conditional>
+    </section>
+</xml>
+</macros>
diff -r 3c3cd68d6d5a -r 27396311a314 test-data/common-complicated.cppipe
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/common-complicated.cppipe	Mon May 11 07:45:07 2020 -0400
@@ -0,0 +1,73 @@
+CellProfiler Pipeline: http://www.cellprofiler.org
+Version:3
+DateRevision:319
+GitHash:
+ModuleCount:4
+HasImagePlaneDetails:False
+
+Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    :
+    Filter images?:Images only
+    Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
+
+Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    Extract metadata?:Yes
+    Metadata data type:Text
+    Metadata types:{}
+    Extraction method count:2
+    Metadata extraction method:Extract from file/folder names
+    Metadata source:File name
+    Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)
+    Regular expression to extract from folder name:(?P<folderField1>.*)
+    Extract metadata from:Images matching a rule
+    Select the filtering criteria:and (file does contain "im") (extension does istif)
+    Metadata file location:
+    Match file and image metadata:[]
+    Use case insensitive matching?:No
+    Metadata extraction method:Extract from file/folder names
+    Metadata source:Folder name
+    Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)
+    Regular expression to extract from folder name:(?P<folderField1>.*)_(?P<folderField2>[a-zA-Z0-9]+)
+    Extract metadata from:All images
+    Select the filtering criteria:and (file does contain "")
+    Metadata file location:
+    Match file and image metadata:[]
+    Use case insensitive matching?:No
+
+NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Assign a name to:Images matching rules
+    Select the image type:Grayscale image
+    Name to assign these images:DNA
+    Match metadata:[]
+    Image set matching method:Order
+    Set intensity range from:Image metadata
+    Assignments count:3
+    Single images count:0
+    Maximum intensity:255.0
+    Process as 3D?:No
+    Relative pixel spacing in X:1.0
+    Relative pixel spacing in Y:1.0
+    Relative pixel spacing in Z:1.0
+    Select the rule criteria:and (file does contain "im") (image doesnot ismonochrome)
+    Name to assign these images:DNA
+    Name to assign these objects:Cell
+    Select the image type:Objects
+    Set intensity range from:Image metadata
+    Maximum intensity:255.0
+    Select the rule criteria:and (file does contain "")
+    Name to assign these images:GFP
+    Name to assign these objects:Cell
+    Select the image type:Illumination function
+    Set intensity range from:Image metadata
+    Maximum intensity:255.0
+    Select the rule criteria:or (extension does istif)
+    Name to assign these images:Actin
+    Name to assign these objects:Cell
+    Select the image type:Grayscale image
+    Set intensity range from:Image metadata
+    Maximum intensity:255.0
+
+Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Do you want to group your images?:Yes
+    grouping metadata count:1
+    Metadata category:field1
diff -r 3c3cd68d6d5a -r 27396311a314 test-data/common-nogroup.cppipe
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/common-nogroup.cppipe	Mon May 11 07:45:07 2020 -0400
@@ -0,0 +1,73 @@
+CellProfiler Pipeline: http://www.cellprofiler.org
+Version:3
+DateRevision:319
+GitHash:
+ModuleCount:4
+HasImagePlaneDetails:False
+
+Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    :
+    Filter images?:Images only
+    Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
+
+Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    Extract metadata?:Yes
+    Metadata data type:Text
+    Metadata types:{}
+    Extraction method count:2
+    Metadata extraction method:Extract from file/folder names
+    Metadata source:File name
+    Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)
+    Regular expression to extract from folder name:(?P<folderField1>.*)
+    Extract metadata from:Images matching a rule
+    Select the filtering criteria:and (file does contain "im") (extension does istif)
+    Metadata file location:
+    Match file and image metadata:[]
+    Use case insensitive matching?:No
+    Metadata extraction method:Extract from file/folder names
+    Metadata source:Folder name
+    Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)
+    Regular expression to extract from folder name:(?P<folderField1>.*)_(?P<folderField2>[a-zA-Z0-9]+)
+    Extract metadata from:All images
+    Select the filtering criteria:and (file does contain "")
+    Metadata file location:
+    Match file and image metadata:[]
+    Use case insensitive matching?:No
+
+NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Assign a name to:Images matching rules
+    Select the image type:Grayscale image
+    Name to assign these images:DNA
+    Match metadata:[]
+    Image set matching method:Order
+    Set intensity range from:Image metadata
+    Assignments count:3
+    Single images count:0
+    Maximum intensity:255.0
+    Process as 3D?:No
+    Relative pixel spacing in X:1.0
+    Relative pixel spacing in Y:1.0
+    Relative pixel spacing in Z:1.0
+    Select the rule criteria:and (file does contain "im") (image doesnot ismonochrome)
+    Name to assign these images:DNA
+    Name to assign these objects:Cell
+    Select the image type:Objects
+    Set intensity range from:Image metadata
+    Maximum intensity:255.0
+    Select the rule criteria:and (file does contain "")
+    Name to assign these images:GFP
+    Name to assign these objects:Cell
+    Select the image type:Illumination function
+    Set intensity range from:Image metadata
+    Maximum intensity:255.0
+    Select the rule criteria:or (extension does istif)
+    Name to assign these images:Actin
+    Name to assign these objects:Cell
+    Select the image type:Grayscale image
+    Set intensity range from:Image metadata
+    Maximum intensity:255.0
+
+Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Do you want to group your images?:No
+    grouping metadata count:1
+    Metadata category:None
diff -r 3c3cd68d6d5a -r 27396311a314 test-data/common.cppipe
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/common.cppipe	Mon May 11 07:45:07 2020 -0400
@@ -0,0 +1,53 @@
+CellProfiler Pipeline: http://www.cellprofiler.org
+Version:3
+DateRevision:319
+GitHash:
+ModuleCount:4
+HasImagePlaneDetails:False
+
+Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    :
+    Filter images?:Images only
+    Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
+
+Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    Extract metadata?:Yes
+    Metadata data type:Text
+    Metadata types:{}
+    Extraction method count:1
+    Metadata extraction method:Extract from file/folder names
+    Metadata source:File name
+    Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)
+    Regular expression to extract from folder name:(?P<folderField1>.*)
+    Extract metadata from:All images
+    Select the filtering criteria:and (file does contain "")
+    Metadata file location:
+    Match file and image metadata:[]
+    Use case insensitive matching?:No
+
+NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Assign a name to:Images matching rules
+    Select the image type:Grayscale image
+    Name to assign these images:DNA
+    Match metadata:[]
+    Image set matching method:Order
+    Set intensity range from:Image metadata
+    Assignments count:1
+    Single images count:0
+    Maximum intensity:255.0
+    Process as 3D?:No
+    Relative pixel spacing in X:1.0
+    Relative pixel spacing in Y:1.0
+    Relative pixel spacing in Z:1.0
+    Select the rule criteria:and (file does startwith "im")
+    Name to assign these images:DNA
+    Name to assign these objects:Cell
+    Select the image type:Grayscale image
+    Set intensity range from:Image metadata
+    Select the image type:Grayscale image
+    Maximum intensity:255.0
+
+Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Do you want to group your images?:Yes
+    grouping metadata count:1
+    Metadata category:field1
diff -r 3c3cd68d6d5a -r 27396311a314 test-data/common.txt
--- a/test-data/common.txt	Thu Apr 16 05:29:02 2020 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,53 +0,0 @@
-CellProfiler Pipeline: http://www.cellprofiler.org
-Version:3
-DateRevision:319
-GitHash:
-ModuleCount:4
-HasImagePlaneDetails:False
-
-Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
-    :
-    Filter images?:Images only
-    Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
-
-Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
-    Extract metadata?:Yes
-    Metadata data type:Text
-    Metadata types:{}
-    Extraction method count:1
-    Metadata extraction method:Extract from file/folder names
-    Metadata source:File name
-    Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)
-    Regular expression to extract from folder name:(?P<field1>.*)
-    Extract metadata from:All images
-    Select the filtering criteria:and (file does contain "")
-    Metadata file location:
-    Match file and image metadata:[]
-    Use case insensitive matching?:No
-
-NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
-    Assign a name to:Images matching rules
-    Select the image type:Grayscale image
-    Name to assign these images:DNA
-    Match metadata:[]
-    Image set matching method:Order
-    Set intensity range from:Image metadata
-    Assignments count:1
-    Single images count:0
-    Maximum intensity:255.0
-    Process as 3D?:No
-    Relative pixel spacing in X:1.0
-    Relative pixel spacing in Y:1.0
-    Relative pixel spacing in Z:1.0
-    Select the rule criteria:and (file does startwith "im")
-    Name to assign these images:DNA
-    Name to assign these objects:Cell
-    Select the image type:Grayscale image
-    Set intensity range from:Image metadata
-    Select the image type:Grayscale image
-    Maximum intensity:255.0
-
-Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
-    Do you want to group your images?:Yes
-    grouping metadata count:1
-    Metadata category:Screen
diff -r 3c3cd68d6d5a -r 27396311a314 test-data/convert_objects_to_image.cppipe
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/convert_objects_to_image.cppipe	Mon May 11 07:45:07 2020 -0400
@@ -0,0 +1,59 @@
+CellProfiler Pipeline: http://www.cellprofiler.org
+Version:3
+DateRevision:319
+GitHash:
+ModuleCount:5
+HasImagePlaneDetails:False
+
+Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    :
+    Filter images?:Images only
+    Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
+
+Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    Extract metadata?:Yes
+    Metadata data type:Text
+    Metadata types:{}
+    Extraction method count:1
+    Metadata extraction method:Extract from file/folder names
+    Metadata source:File name
+    Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)
+    Regular expression to extract from folder name:(?P<folderField1>.*)
+    Extract metadata from:All images
+    Select the filtering criteria:and (file does contain "")
+    Metadata file location:
+    Match file and image metadata:[]
+    Use case insensitive matching?:No
+
+NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Assign a name to:Images matching rules
+    Select the image type:Grayscale image
+    Name to assign these images:DNA
+    Match metadata:[]
+    Image set matching method:Order
+    Set intensity range from:Image metadata
+    Assignments count:1
+    Single images count:0
+    Maximum intensity:255.0
+    Process as 3D?:No
+    Relative pixel spacing in X:1.0
+    Relative pixel spacing in Y:1.0
+    Relative pixel spacing in Z:1.0
+    Select the rule criteria:and (file does startwith "im")
+    Name to assign these images:DNA
+    Name to assign these objects:Cell
+    Select the image type:Grayscale image
+    Set intensity range from:Image metadata
+    Select the image type:Grayscale image
+    Maximum intensity:255.0
+
+Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Do you want to group your images?:Yes
+    grouping metadata count:1
+    Metadata category:field1
+
+ConvertObjectsToImage:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:1|show_window:True|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Select the input objects:Nuclei
+    Name the output image:MaskNuclei
+    Select the color format:Binary (black & white)
+    Select the colormap:Default
diff -r 3c3cd68d6d5a -r 27396311a314 test-data/convert_objects_to_image.txt
--- a/test-data/convert_objects_to_image.txt	Thu Apr 16 05:29:02 2020 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,59 +0,0 @@
-CellProfiler Pipeline: http://www.cellprofiler.org
-Version:3
-DateRevision:319
-GitHash:
-ModuleCount:5
-HasImagePlaneDetails:False
-
-Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
-    :
-    Filter images?:Images only
-    Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
-
-Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
-    Extract metadata?:Yes
-    Metadata data type:Text
-    Metadata types:{}
-    Extraction method count:1
-    Metadata extraction method:Extract from file/folder names
-    Metadata source:File name
-    Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)
-    Regular expression to extract from folder name:(?P<field1>.*)
-    Extract metadata from:All images
-    Select the filtering criteria:and (file does contain "")
-    Metadata file location:
-    Match file and image metadata:[]
-    Use case insensitive matching?:No
-
-NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
-    Assign a name to:Images matching rules
-    Select the image type:Grayscale image
-    Name to assign these images:DNA
-    Match metadata:[]
-    Image set matching method:Order
-    Set intensity range from:Image metadata
-    Assignments count:1
-    Single images count:0
-    Maximum intensity:255.0
-    Process as 3D?:No
-    Relative pixel spacing in X:1.0
-    Relative pixel spacing in Y:1.0
-    Relative pixel spacing in Z:1.0
-    Select the rule criteria:and (file does startwith "im")
-    Name to assign these images:DNA
-    Name to assign these objects:Cell
-    Select the image type:Grayscale image
-    Set intensity range from:Image metadata
-    Select the image type:Grayscale image
-    Maximum intensity:255.0
-
-Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
-    Do you want to group your images?:Yes
-    grouping metadata count:1
-    Metadata category:Screen
-
-ConvertObjectsToImage:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:1|show_window:True|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
-    Select the input objects:Nuclei
-    Name the output image:MaskNuclei
-    Select the color format:Binary (black & white)
-    Select the colormap:Default
diff -r 3c3cd68d6d5a -r 27396311a314 test-data/display_data_on_image.cppipe
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/display_data_on_image.cppipe	Mon May 11 07:45:07 2020 -0400
@@ -0,0 +1,70 @@
+CellProfiler Pipeline: http://www.cellprofiler.org
+Version:3
+DateRevision:319
+GitHash:
+ModuleCount:5
+HasImagePlaneDetails:False
+
+Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    :
+    Filter images?:Images only
+    Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
+
+Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    Extract metadata?:Yes
+    Metadata data type:Text
+    Metadata types:{}
+    Extraction method count:1
+    Metadata extraction method:Extract from file/folder names
+    Metadata source:File name
+    Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)
+    Regular expression to extract from folder name:(?P<folderField1>.*)
+    Extract metadata from:All images
+    Select the filtering criteria:and (file does contain "")
+    Metadata file location:
+    Match file and image metadata:[]
+    Use case insensitive matching?:No
+
+NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Assign a name to:Images matching rules
+    Select the image type:Grayscale image
+    Name to assign these images:DNA
+    Match metadata:[]
+    Image set matching method:Order
+    Set intensity range from:Image metadata
+    Assignments count:1
+    Single images count:0
+    Maximum intensity:255.0
+    Process as 3D?:No
+    Relative pixel spacing in X:1.0
+    Relative pixel spacing in Y:1.0
+    Relative pixel spacing in Z:1.0
+    Select the rule criteria:and (file does startwith "im")
+    Name to assign these images:DNA
+    Name to assign these objects:Cell
+    Select the image type:Grayscale image
+    Set intensity range from:Image metadata
+    Select the image type:Grayscale image
+    Maximum intensity:255.0
+
+Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Do you want to group your images?:Yes
+    grouping metadata count:1
+    Metadata category:field1
+
+DisplayDataOnImage:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:6|show_window:False|notes:\x5B\'Add nuclei id as label\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Display object or image measurements?:Object
+    Select the input objects:Nuclei
+    Measurement to display:Number_Object_Number
+    Select the image on which to display the measurements:DNA
+    Text color:#ff0000
+    Name the output image that has the measurements displayed:ImageDisplay
+    Font size (points):11
+    Number of decimals:0
+    Image elements to save:Image
+    Annotation offset (in pixels):0
+    Display mode:Text
+    Color map:Default
+    Display background image?:Yes
+    Color map scale:Use this image's measurement range
+    Color map range:0.0,1.0
diff -r 3c3cd68d6d5a -r 27396311a314 test-data/display_data_on_image.txt
--- a/test-data/display_data_on_image.txt	Thu Apr 16 05:29:02 2020 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,70 +0,0 @@
-CellProfiler Pipeline: http://www.cellprofiler.org
-Version:3
-DateRevision:319
-GitHash:
-ModuleCount:5
-HasImagePlaneDetails:False
-
-Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
-    :
-    Filter images?:Images only
-    Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
-
-Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
-    Extract metadata?:Yes
-    Metadata data type:Text
-    Metadata types:{}
-    Extraction method count:1
-    Metadata extraction method:Extract from file/folder names
-    Metadata source:File name
-    Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)
-    Regular expression to extract from folder name:(?P<field1>.*)
-    Extract metadata from:All images
-    Select the filtering criteria:and (file does contain "")
-    Metadata file location:
-    Match file and image metadata:[]
-    Use case insensitive matching?:No
-
-NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
-    Assign a name to:Images matching rules
-    Select the image type:Grayscale image
-    Name to assign these images:DNA
-    Match metadata:[]
-    Image set matching method:Order
-    Set intensity range from:Image metadata
-    Assignments count:1
-    Single images count:0
-    Maximum intensity:255.0
-    Process as 3D?:No
-    Relative pixel spacing in X:1.0
-    Relative pixel spacing in Y:1.0
-    Relative pixel spacing in Z:1.0
-    Select the rule criteria:and (file does startwith "im")
-    Name to assign these images:DNA
-    Name to assign these objects:Cell
-    Select the image type:Grayscale image
-    Set intensity range from:Image metadata
-    Select the image type:Grayscale image
-    Maximum intensity:255.0
-
-Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
-    Do you want to group your images?:Yes
-    grouping metadata count:1
-    Metadata category:Screen
-
-DisplayDataOnImage:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:6|show_window:False|notes:\x5B\'Add nuclei id as label\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
-    Display object or image measurements?:Object
-    Select the input objects:Nuclei
-    Measurement to display:Number_Object_Number
-    Select the image on which to display the measurements:DNA
-    Text color:#ff0000
-    Name the output image that has the measurements displayed:ImageDisplay
-    Font size (points):11
-    Number of decimals:0
-    Image elements to save:Image
-    Annotation offset (in pixels):0
-    Display mode:Text
-    Color map:Default
-    Display background image?:Yes
-    Color map scale:Use this image's measurement range
-    Color map range:0.0,1.0
diff -r 3c3cd68d6d5a -r 27396311a314 test-data/enhance_or_suppress_features.cppipe
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/enhance_or_suppress_features.cppipe	Mon May 11 07:45:07 2020 -0400
@@ -0,0 +1,66 @@
+CellProfiler Pipeline: http://www.cellprofiler.org
+Version:3
+DateRevision:319
+GitHash:
+ModuleCount:5
+HasImagePlaneDetails:False
+
+Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    :
+    Filter images?:Images only
+    Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
+
+Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    Extract metadata?:Yes
+    Metadata data type:Text
+    Metadata types:{}
+    Extraction method count:1
+    Metadata extraction method:Extract from file/folder names
+    Metadata source:File name
+    Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)
+    Regular expression to extract from folder name:(?P<folderField1>.*)
+    Extract metadata from:All images
+    Select the filtering criteria:and (file does contain "")
+    Metadata file location:
+    Match file and image metadata:[]
+    Use case insensitive matching?:No
+
+NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Assign a name to:Images matching rules
+    Select the image type:Grayscale image
+    Name to assign these images:DNA
+    Match metadata:[]
+    Image set matching method:Order
+    Set intensity range from:Image metadata
+    Assignments count:1
+    Single images count:0
+    Maximum intensity:255.0
+    Process as 3D?:No
+    Relative pixel spacing in X:1.0
+    Relative pixel spacing in Y:1.0
+    Relative pixel spacing in Z:1.0
+    Select the rule criteria:and (file does startwith "im")
+    Name to assign these images:DNA
+    Name to assign these objects:Cell
+    Select the image type:Grayscale image
+    Set intensity range from:Image metadata
+    Select the image type:Grayscale image
+    Maximum intensity:255.0
+
+Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Do you want to group your images?:Yes
+    grouping metadata count:1
+    Metadata category:field1
+
+EnhanceOrSuppressFeatures:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:6|show_window:False|notes:\x5B\'Identify nucleoli\', \'PARAMS\x3A Range of hole sizes'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Select the input image:DNA
+    Name the output image:DNAdarkholes
+    Select the operation:Enhance
+    Feature size:10
+    Feature type:Dark holes
+    Range of hole sizes:1,15
+    Smoothing scale:2.0
+    Shear angle:0.0
+    Decay:0.95
+    Enhancement method:Tubeness
+    Speed and accuracy:Fast
diff -r 3c3cd68d6d5a -r 27396311a314 test-data/enhance_or_suppress_features.txt
--- a/test-data/enhance_or_suppress_features.txt	Thu Apr 16 05:29:02 2020 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,66 +0,0 @@
-CellProfiler Pipeline: http://www.cellprofiler.org
-Version:3
-DateRevision:319
-GitHash:
-ModuleCount:5
-HasImagePlaneDetails:False
-
-Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
-    :
-    Filter images?:Images only
-    Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
-
-Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
-    Extract metadata?:Yes
-    Metadata data type:Text
-    Metadata types:{}
-    Extraction method count:1
-    Metadata extraction method:Extract from file/folder names
-    Metadata source:File name
-    Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)
-    Regular expression to extract from folder name:(?P<field1>.*)
-    Extract metadata from:All images
-    Select the filtering criteria:and (file does contain "")
-    Metadata file location:
-    Match file and image metadata:[]
-    Use case insensitive matching?:No
-
-NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
-    Assign a name to:Images matching rules
-    Select the image type:Grayscale image
-    Name to assign these images:DNA
-    Match metadata:[]
-    Image set matching method:Order
-    Set intensity range from:Image metadata
-    Assignments count:1
-    Single images count:0
-    Maximum intensity:255.0
-    Process as 3D?:No
-    Relative pixel spacing in X:1.0
-    Relative pixel spacing in Y:1.0
-    Relative pixel spacing in Z:1.0
-    Select the rule criteria:and (file does startwith "im")
-    Name to assign these images:DNA
-    Name to assign these objects:Cell
-    Select the image type:Grayscale image
-    Set intensity range from:Image metadata
-    Select the image type:Grayscale image
-    Maximum intensity:255.0
-
-Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
-    Do you want to group your images?:Yes
-    grouping metadata count:1
-    Metadata category:Screen
-
-EnhanceOrSuppressFeatures:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:6|show_window:False|notes:\x5B\'Identify nucleoli\', \'PARAMS\x3A Range of hole sizes'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
-    Select the input image:DNA
-    Name the output image:DNAdarkholes
-    Select the operation:Enhance
-    Feature size:10
-    Feature type:Dark holes
-    Range of hole sizes:1,15
-    Smoothing scale:2.0
-    Shear angle:0.0
-    Decay:0.95
-    Enhancement method:Tubeness
-    Speed and accuracy:Fast
diff -r 3c3cd68d6d5a -r 27396311a314 test-data/export_to_spreadsheet.cppipe
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/export_to_spreadsheet.cppipe	Mon May 11 07:45:07 2020 -0400
@@ -0,0 +1,76 @@
+CellProfiler Pipeline: http://www.cellprofiler.org
+Version:3
+DateRevision:319
+GitHash:
+ModuleCount:5
+HasImagePlaneDetails:False
+
+Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    :
+    Filter images?:Images only
+    Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
+
+Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    Extract metadata?:Yes
+    Metadata data type:Text
+    Metadata types:{}
+    Extraction method count:1
+    Metadata extraction method:Extract from file/folder names
+    Metadata source:File name
+    Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)
+    Regular expression to extract from folder name:(?P<folderField1>.*)
+    Extract metadata from:All images
+    Select the filtering criteria:and (file does contain "")
+    Metadata file location:
+    Match file and image metadata:[]
+    Use case insensitive matching?:No
+
+NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Assign a name to:Images matching rules
+    Select the image type:Grayscale image
+    Name to assign these images:DNA
+    Match metadata:[]
+    Image set matching method:Order
+    Set intensity range from:Image metadata
+    Assignments count:1
+    Single images count:0
+    Maximum intensity:255.0
+    Process as 3D?:No
+    Relative pixel spacing in X:1.0
+    Relative pixel spacing in Y:1.0
+    Relative pixel spacing in Z:1.0
+    Select the rule criteria:and (file does startwith "im")
+    Name to assign these images:DNA
+    Name to assign these objects:Cell
+    Select the image type:Grayscale image
+    Set intensity range from:Image metadata
+    Select the image type:Grayscale image
+    Maximum intensity:255.0
+
+Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Do you want to group your images?:Yes
+    grouping metadata count:1
+    Metadata category:field1
+
+ExportToSpreadsheet:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:12|show_window:True|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Select the column delimiter:Tab
+    Add image metadata columns to your object data file?:Yes
+    Select the measurements to export:No
+    Calculate the per-image mean values for object measurements?:Yes
+    Calculate the per-image median values for object measurements?:Yes
+    Calculate the per-image standard deviation values for object measurements?:Yes
+    Output file location:Default Output Folder\x7C
+    Create a GenePattern GCT file?:No
+    Select source of sample row name:Metadata
+    Select the image to use as the identifier:None
+    Select the metadata to use as the identifier:None
+    Export all measurement types?:Yes
+    Press button to select measurements:
+    Representation of Nan/Inf:NaN
+    Add a prefix to file names?:No
+    Filename prefix:MyPrefix_
+    Overwrite existing files without warning?:Yes
+    Data to export:Do not use
+    Combine these object measurements with those of the previous object?:No
+    File name:DATA.csv
+    Use the object name for the file name?:Yes
diff -r 3c3cd68d6d5a -r 27396311a314 test-data/export_to_spreadsheet.txt
--- a/test-data/export_to_spreadsheet.txt	Thu Apr 16 05:29:02 2020 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,76 +0,0 @@
-CellProfiler Pipeline: http://www.cellprofiler.org
-Version:3
-DateRevision:319
-GitHash:
-ModuleCount:5
-HasImagePlaneDetails:False
-
-Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
-    :
-    Filter images?:Images only
-    Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
-
-Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
-    Extract metadata?:Yes
-    Metadata data type:Text
-    Metadata types:{}
-    Extraction method count:1
-    Metadata extraction method:Extract from file/folder names
-    Metadata source:File name
-    Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)
-    Regular expression to extract from folder name:(?P<field1>.*)
-    Extract metadata from:All images
-    Select the filtering criteria:and (file does contain "")
-    Metadata file location:
-    Match file and image metadata:[]
-    Use case insensitive matching?:No
-
-NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
-    Assign a name to:Images matching rules
-    Select the image type:Grayscale image
-    Name to assign these images:DNA
-    Match metadata:[]
-    Image set matching method:Order
-    Set intensity range from:Image metadata
-    Assignments count:1
-    Single images count:0
-    Maximum intensity:255.0
-    Process as 3D?:No
-    Relative pixel spacing in X:1.0
-    Relative pixel spacing in Y:1.0
-    Relative pixel spacing in Z:1.0
-    Select the rule criteria:and (file does startwith "im")
-    Name to assign these images:DNA
-    Name to assign these objects:Cell
-    Select the image type:Grayscale image
-    Set intensity range from:Image metadata
-    Select the image type:Grayscale image
-    Maximum intensity:255.0
-
-Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
-    Do you want to group your images?:Yes
-    grouping metadata count:1
-    Metadata category:Screen
-
-ExportToSpreadsheet:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:12|show_window:True|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
-    Select the column delimiter:Tab
-    Add image metadata columns to your object data file?:Yes
-    Select the measurements to export:No
-    Calculate the per-image mean values for object measurements?:Yes
-    Calculate the per-image median values for object measurements?:Yes
-    Calculate the per-image standard deviation values for object measurements?:Yes
-    Output file location:Default Output Folder\x7C
-    Create a GenePattern GCT file?:No
-    Select source of sample row name:Metadata
-    Select the image to use as the identifier:None
-    Select the metadata to use as the identifier:None
-    Export all measurement types?:Yes
-    Press button to select measurements:
-    Representation of Nan/Inf:NaN
-    Add a prefix to file names?:No
-    Filename prefix:MyPrefix_
-    Overwrite existing files without warning?:Yes
-    Data to export:Do not use
-    Combine these object measurements with those of the previous object?:No
-    File name:DATA.csv
-    Use the object name for the file name?:Yes
diff -r 3c3cd68d6d5a -r 27396311a314 test-data/export_to_spreadsheet_create_gene.cppipe
diff -r 3c3cd68d6d5a -r 27396311a314 test-data/export_to_spreadsheet_create_gene_image_filename.cppipe
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/export_to_spreadsheet_create_gene_image_filename.cppipe	Mon May 11 07:45:07 2020 -0400
@@ -0,0 +1,76 @@
+CellProfiler Pipeline: http://www.cellprofiler.org
+Version:3
+DateRevision:319
+GitHash:
+ModuleCount:5
+HasImagePlaneDetails:False
+
+Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    :
+    Filter images?:Images only
+    Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
+
+Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    Extract metadata?:Yes
+    Metadata data type:Text
+    Metadata types:{}
+    Extraction method count:1
+    Metadata extraction method:Extract from file/folder names
+    Metadata source:File name
+    Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)
+    Regular expression to extract from folder name:(?P<folderField1>.*)
+    Extract metadata from:All images
+    Select the filtering criteria:and (file does contain "")
+    Metadata file location:
+    Match file and image metadata:[]
+    Use case insensitive matching?:No
+
+NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Assign a name to:Images matching rules
+    Select the image type:Grayscale image
+    Name to assign these images:DNA
+    Match metadata:[]
+    Image set matching method:Order
+    Set intensity range from:Image metadata
+    Assignments count:1
+    Single images count:0
+    Maximum intensity:255.0
+    Process as 3D?:No
+    Relative pixel spacing in X:1.0
+    Relative pixel spacing in Y:1.0
+    Relative pixel spacing in Z:1.0
+    Select the rule criteria:and (file does startwith "im")
+    Name to assign these images:DNA
+    Name to assign these objects:Cell
+    Select the image type:Grayscale image
+    Set intensity range from:Image metadata
+    Select the image type:Grayscale image
+    Maximum intensity:255.0
+
+Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Do you want to group your images?:Yes
+    grouping metadata count:1
+    Metadata category:field1
+
+ExportToSpreadsheet:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:12|show_window:True|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Select the column delimiter:Tab
+    Add image metadata columns to your object data file?:Yes
+    Select the measurements to export:No
+    Calculate the per-image mean values for object measurements?:Yes
+    Calculate the per-image median values for object measurements?:Yes
+    Calculate the per-image standard deviation values for object measurements?:Yes
+    Output file location:Default Output Folder\x7C
+    Create a GenePattern GCT file?:Yes
+    Select source of sample row name:Image filename
+    Select the image to use as the identifier:DNA
+    Select the metadata to use as the identifier:None
+    Export all measurement types?:No
+    Press button to select measurements:
+    Representation of Nan/Inf:NaN
+    Add a prefix to file names?:Yes
+    Filename prefix:MyExpt_
+    Overwrite existing files without warning?:Yes
+    Data to export:Image
+    Combine these object measurements with those of the previous object?:No
+    File name:data.csv
+    Use the object name for the file name?:No
diff -r 3c3cd68d6d5a -r 27396311a314 test-data/export_to_spreadsheet_create_gene_metadata.cppipe
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/export_to_spreadsheet_create_gene_metadata.cppipe	Mon May 11 07:45:07 2020 -0400
@@ -0,0 +1,76 @@
+CellProfiler Pipeline: http://www.cellprofiler.org
+Version:3
+DateRevision:319
+GitHash:
+ModuleCount:5
+HasImagePlaneDetails:False
+
+Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    :
+    Filter images?:Images only
+    Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
+
+Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    Extract metadata?:Yes
+    Metadata data type:Text
+    Metadata types:{}
+    Extraction method count:1
+    Metadata extraction method:Extract from file/folder names
+    Metadata source:File name
+    Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)
+    Regular expression to extract from folder name:(?P<folderField1>.*)
+    Extract metadata from:All images
+    Select the filtering criteria:and (file does contain "")
+    Metadata file location:
+    Match file and image metadata:[]
+    Use case insensitive matching?:No
+
+NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Assign a name to:Images matching rules
+    Select the image type:Grayscale image
+    Name to assign these images:DNA
+    Match metadata:[]
+    Image set matching method:Order
+    Set intensity range from:Image metadata
+    Assignments count:1
+    Single images count:0
+    Maximum intensity:255.0
+    Process as 3D?:No
+    Relative pixel spacing in X:1.0
+    Relative pixel spacing in Y:1.0
+    Relative pixel spacing in Z:1.0
+    Select the rule criteria:and (file does startwith "im")
+    Name to assign these images:DNA
+    Name to assign these objects:Cell
+    Select the image type:Grayscale image
+    Set intensity range from:Image metadata
+    Select the image type:Grayscale image
+    Maximum intensity:255.0
+
+Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Do you want to group your images?:Yes
+    grouping metadata count:1
+    Metadata category:field1
+
+ExportToSpreadsheet:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:12|show_window:True|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Select the column delimiter:Tab
+    Add image metadata columns to your object data file?:Yes
+    Select the measurements to export:No
+    Calculate the per-image mean values for object measurements?:Yes
+    Calculate the per-image median values for object measurements?:Yes
+    Calculate the per-image standard deviation values for object measurements?:Yes
+    Output file location:Default Output Folder\x7C
+    Create a GenePattern GCT file?:Yes
+    Select source of sample row name:Metadata
+    Select the image to use as the identifier:None
+    Select the metadata to use as the identifier:FileName_DNA
+    Export all measurement types?:Yes
+    Press button to select measurements:
+    Representation of Nan/Inf:NaN
+    Add a prefix to file names?:No
+    Filename prefix:MyPrefix_
+    Overwrite existing files without warning?:Yes
+    Data to export:Do not use
+    Combine these object measurements with those of the previous object?:No
+    File name:DATA.csv
+    Use the object name for the file name?:Yes
diff -r 3c3cd68d6d5a -r 27396311a314 test-data/export_to_spreadsheet_multi.cppipe
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/export_to_spreadsheet_multi.cppipe	Mon May 11 07:45:07 2020 -0400
@@ -0,0 +1,80 @@
+CellProfiler Pipeline: http://www.cellprofiler.org
+Version:3
+DateRevision:319
+GitHash:
+ModuleCount:5
+HasImagePlaneDetails:False
+
+Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    :
+    Filter images?:Images only
+    Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
+
+Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    Extract metadata?:Yes
+    Metadata data type:Text
+    Metadata types:{}
+    Extraction method count:1
+    Metadata extraction method:Extract from file/folder names
+    Metadata source:File name
+    Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)
+    Regular expression to extract from folder name:(?P<folderField1>.*)
+    Extract metadata from:All images
+    Select the filtering criteria:and (file does contain "")
+    Metadata file location:
+    Match file and image metadata:[]
+    Use case insensitive matching?:No
+
+NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Assign a name to:Images matching rules
+    Select the image type:Grayscale image
+    Name to assign these images:DNA
+    Match metadata:[]
+    Image set matching method:Order
+    Set intensity range from:Image metadata
+    Assignments count:1
+    Single images count:0
+    Maximum intensity:255.0
+    Process as 3D?:No
+    Relative pixel spacing in X:1.0
+    Relative pixel spacing in Y:1.0
+    Relative pixel spacing in Z:1.0
+    Select the rule criteria:and (file does startwith "im")
+    Name to assign these images:DNA
+    Name to assign these objects:Cell
+    Select the image type:Grayscale image
+    Set intensity range from:Image metadata
+    Select the image type:Grayscale image
+    Maximum intensity:255.0
+
+Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Do you want to group your images?:Yes
+    grouping metadata count:1
+    Metadata category:field1
+
+ExportToSpreadsheet:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:12|show_window:True|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Select the column delimiter:Tab
+    Add image metadata columns to your object data file?:Yes
+    Select the measurements to export:No
+    Calculate the per-image mean values for object measurements?:Yes
+    Calculate the per-image median values for object measurements?:Yes
+    Calculate the per-image standard deviation values for object measurements?:Yes
+    Output file location:Default Output Folder\x7C
+    Create a GenePattern GCT file?:Yes
+    Select source of sample row name:Image filename
+    Select the image to use as the identifier:DNA
+    Select the metadata to use as the identifier:None
+    Export all measurement types?:No
+    Press button to select measurements:
+    Representation of Nan/Inf:NaN
+    Add a prefix to file names?:Yes
+    Filename prefix:MyExpt_
+    Overwrite existing files without warning?:Yes
+    Data to export:Image
+    Combine these object measurements with those of the previous object?:No
+    File name:data.csv
+    Use the object name for the file name?:No
+    Data to export:Experiment
+    Combine these object measurements with those of the previous object?:No
+    File name:DATA.csv
+    Use the object name for the file name?:Yes
diff -r 3c3cd68d6d5a -r 27396311a314 test-data/gray_to_color.cppipe
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gray_to_color.cppipe	Mon May 11 07:45:07 2020 -0400
@@ -0,0 +1,75 @@
+CellProfiler Pipeline: http://www.cellprofiler.org
+Version:3
+DateRevision:319
+GitHash:
+ModuleCount:5
+HasImagePlaneDetails:False
+
+Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    :
+    Filter images?:Images only
+    Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
+
+Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    Extract metadata?:Yes
+    Metadata data type:Text
+    Metadata types:{}
+    Extraction method count:1
+    Metadata extraction method:Extract from file/folder names
+    Metadata source:File name
+    Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)
+    Regular expression to extract from folder name:(?P<folderField1>.*)
+    Extract metadata from:All images
+    Select the filtering criteria:and (file does contain "")
+    Metadata file location:
+    Match file and image metadata:[]
+    Use case insensitive matching?:No
+
+NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Assign a name to:Images matching rules
+    Select the image type:Grayscale image
+    Name to assign these images:DNA
+    Match metadata:[]
+    Image set matching method:Order
+    Set intensity range from:Image metadata
+    Assignments count:1
+    Single images count:0
+    Maximum intensity:255.0
+    Process as 3D?:No
+    Relative pixel spacing in X:1.0
+    Relative pixel spacing in Y:1.0
+    Relative pixel spacing in Z:1.0
+    Select the rule criteria:and (file does startwith "im")
+    Name to assign these images:DNA
+    Name to assign these objects:Cell
+    Select the image type:Grayscale image
+    Set intensity range from:Image metadata
+    Select the image type:Grayscale image
+    Maximum intensity:255.0
+
+Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Do you want to group your images?:Yes
+    grouping metadata count:1
+    Metadata category:field1
+
+GrayToColor:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:3|show_window:False|notes:\x5B\'Combine masks nuclei + nucleoli with colors\'\x5D|batch_state:array(\x5B], dtype=uint8)|enabled:True|wants_pause:False]
+    Select a color scheme:RGB
+    Select the image to be colored red:MaskNucleoli
+    Select the image to be colored green:Leave this black
+    Select the image to be colored blue:MaskNuclei
+    Name the output image:CombinedMask
+    Relative weight for the red image:0.8
+    Relative weight for the green image:1.0
+    Relative weight for the blue image:0.5
+    Select the image to be colored cyan:Leave this black
+    Select the image to be colored magenta:Leave this black
+    Select the image to be colored yellow:Leave this black
+    Select the image that determines brightness:Leave this black
+    Relative weight for the cyan image:1.0
+    Relative weight for the magenta image:1.0
+    Relative weight for the yellow image:1.0
+    Relative weight for the brightness image:1.0
+    Hidden:1
+    Image name:None
+    Color:#FF0000
+    Weight:1.0
diff -r 3c3cd68d6d5a -r 27396311a314 test-data/gray_to_color.txt
--- a/test-data/gray_to_color.txt	Thu Apr 16 05:29:02 2020 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,75 +0,0 @@
-CellProfiler Pipeline: http://www.cellprofiler.org
-Version:3
-DateRevision:319
-GitHash:
-ModuleCount:5
-HasImagePlaneDetails:False
-
-Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
-    :
-    Filter images?:Images only
-    Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
-
-Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
-    Extract metadata?:Yes
-    Metadata data type:Text
-    Metadata types:{}
-    Extraction method count:1
-    Metadata extraction method:Extract from file/folder names
-    Metadata source:File name
-    Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)
-    Regular expression to extract from folder name:(?P<field1>.*)
-    Extract metadata from:All images
-    Select the filtering criteria:and (file does contain "")
-    Metadata file location:
-    Match file and image metadata:[]
-    Use case insensitive matching?:No
-
-NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
-    Assign a name to:Images matching rules
-    Select the image type:Grayscale image
-    Name to assign these images:DNA
-    Match metadata:[]
-    Image set matching method:Order
-    Set intensity range from:Image metadata
-    Assignments count:1
-    Single images count:0
-    Maximum intensity:255.0
-    Process as 3D?:No
-    Relative pixel spacing in X:1.0
-    Relative pixel spacing in Y:1.0
-    Relative pixel spacing in Z:1.0
-    Select the rule criteria:and (file does startwith "im")
-    Name to assign these images:DNA
-    Name to assign these objects:Cell
-    Select the image type:Grayscale image
-    Set intensity range from:Image metadata
-    Select the image type:Grayscale image
-    Maximum intensity:255.0
-
-Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
-    Do you want to group your images?:Yes
-    grouping metadata count:1
-    Metadata category:Screen
-
-GrayToColor:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:3|show_window:False|notes:\x5B\'Combine masks nuclei + nucleoli with colors\'\x5D|batch_state:array(\x5B], dtype=uint8)|enabled:True|wants_pause:False]
-    Select a color scheme:RGB
-    Select the image to be colored red:MaskNucleoli
-    Select the image to be colored green:Leave this black
-    Select the image to be colored blue:MaskNuclei
-    Name the output image:CombinedMask
-    Relative weight for the red image:0.8
-    Relative weight for the green image:1.0
-    Relative weight for the blue image:0.5
-    Select the image to be colored cyan:Leave this black
-    Select the image to be colored magenta:Leave this black
-    Select the image to be colored yellow:Leave this black
-    Select the image that determines brightness:Leave this black
-    Relative weight for the cyan image:1.0
-    Relative weight for the magenta image:1.0
-    Relative weight for the yellow image:1.0
-    Relative weight for the brightness image:1.0
-    Hidden:1
-    Image name:None
-    Color:#FF0000
-    Weight:1.0
diff -r 3c3cd68d6d5a -r 27396311a314 test-data/identify_primary_objects.cppipe
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/identify_primary_objects.cppipe	Mon May 11 07:45:07 2020 -0400
@@ -0,0 +1,88 @@
+CellProfiler Pipeline: http://www.cellprofiler.org
+Version:3
+DateRevision:319
+GitHash:
+ModuleCount:5
+HasImagePlaneDetails:False
+
+Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    :
+    Filter images?:Images only
+    Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
+
+Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    Extract metadata?:Yes
+    Metadata data type:Text
+    Metadata types:{}
+    Extraction method count:1
+    Metadata extraction method:Extract from file/folder names
+    Metadata source:File name
+    Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)
+    Regular expression to extract from folder name:(?P<folderField1>.*)
+    Extract metadata from:All images
+    Select the filtering criteria:and (file does contain "")
+    Metadata file location:
+    Match file and image metadata:[]
+    Use case insensitive matching?:No
+
+NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Assign a name to:Images matching rules
+    Select the image type:Grayscale image
+    Name to assign these images:DNA
+    Match metadata:[]
+    Image set matching method:Order
+    Set intensity range from:Image metadata
+    Assignments count:1
+    Single images count:0
+    Maximum intensity:255.0
+    Process as 3D?:No
+    Relative pixel spacing in X:1.0
+    Relative pixel spacing in Y:1.0
+    Relative pixel spacing in Z:1.0
+    Select the rule criteria:and (file does startwith "im")
+    Name to assign these images:DNA
+    Name to assign these objects:Cell
+    Select the image type:Grayscale image
+    Set intensity range from:Image metadata
+    Select the image type:Grayscale image
+    Maximum intensity:255.0
+
+Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Do you want to group your images?:Yes
+    grouping metadata count:1
+    Metadata category:field1
+
+IdentifyPrimaryObjects:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:13|show_window:True|notes:\x5B\'Identify the nuclei from the DNA channel.\', \'PARAMS\x3A\', \'- Typical diameter of objects (Min,Max)\', \'- Method to distinguish clumped objects\x3A Shape/None. With Shape, the distance between the 2 centers can be changed.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Select the input image:DNA
+    Name the primary objects to be identified:Nuclei
+    Typical diameter of objects, in pixel units (Min,Max):15,200
+    Discard objects outside the diameter range?:Yes
+    Discard objects touching the border of the image?:Yes
+    Method to distinguish clumped objects:Shape
+    Method to draw dividing lines between clumped objects:Shape
+    Size of smoothing filter:0
+    Suppress local maxima that are closer than this minimum allowed distance:7
+    Speed up by using lower-resolution image to find local maxima?:Yes
+    Fill holes in identified objects?:After both thresholding and declumping
+    Automatically calculate size of smoothing filter for declumping?:Yes
+    Automatically calculate minimum allowed distance between local maxima?:Yes
+    Handling of objects if excessive number of objects identified:Continue
+    Maximum number of objects:500
+    Use advanced settings?:Yes
+    Threshold settings version:10
+    Threshold strategy:Global
+    Thresholding method:Otsu
+    Threshold smoothing scale:1.3488
+    Threshold correction factor:0.9
+    Lower and upper bounds on threshold:0.0,1.0
+    Manual threshold:0
+    Select the measurement to threshold with:None
+    Two-class or three-class thresholding?:Two classes
+    Assign pixels in the middle intensity class to the foreground or the background?:Foreground
+    Size of adaptive window:500
+    Lower outlier fraction:0.05
+    Upper outlier fraction:0.05
+    Averaging method:Mean
+    Variance method:Standard deviation
+    # of deviations:2.0
+    Thresholding method:Otsu
diff -r 3c3cd68d6d5a -r 27396311a314 test-data/identify_primary_objects.txt
--- a/test-data/identify_primary_objects.txt	Thu Apr 16 05:29:02 2020 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,88 +0,0 @@
-CellProfiler Pipeline: http://www.cellprofiler.org
-Version:3
-DateRevision:319
-GitHash:
-ModuleCount:5
-HasImagePlaneDetails:False
-
-Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
-    :
-    Filter images?:Images only
-    Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
-
-Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
-    Extract metadata?:Yes
-    Metadata data type:Text
-    Metadata types:{}
-    Extraction method count:1
-    Metadata extraction method:Extract from file/folder names
-    Metadata source:File name
-    Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)
-    Regular expression to extract from folder name:(?P<field1>.*)
-    Extract metadata from:All images
-    Select the filtering criteria:and (file does contain "")
-    Metadata file location:
-    Match file and image metadata:[]
-    Use case insensitive matching?:No
-
-NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
-    Assign a name to:Images matching rules
-    Select the image type:Grayscale image
-    Name to assign these images:DNA
-    Match metadata:[]
-    Image set matching method:Order
-    Set intensity range from:Image metadata
-    Assignments count:1
-    Single images count:0
-    Maximum intensity:255.0
-    Process as 3D?:No
-    Relative pixel spacing in X:1.0
-    Relative pixel spacing in Y:1.0
-    Relative pixel spacing in Z:1.0
-    Select the rule criteria:and (file does startwith "im")
-    Name to assign these images:DNA
-    Name to assign these objects:Cell
-    Select the image type:Grayscale image
-    Set intensity range from:Image metadata
-    Select the image type:Grayscale image
-    Maximum intensity:255.0
-
-Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
-    Do you want to group your images?:Yes
-    grouping metadata count:1
-    Metadata category:Screen
-
-IdentifyPrimaryObjects:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:13|show_window:True|notes:\x5B\'Identify the nuclei from the DNA channel.\', \'PARAMS\x3A\', \'- Typical diameter of objects (Min,Max)\', \'- Method to distinguish clumped objects\x3A Shape/None. With Shape, the distance between the 2 centers can be changed.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
-    Select the input image:DNA
-    Name the primary objects to be identified:Nuclei
-    Typical diameter of objects, in pixel units (Min,Max):15,200
-    Discard objects outside the diameter range?:Yes
-    Discard objects touching the border of the image?:Yes
-    Method to distinguish clumped objects:Shape
-    Method to draw dividing lines between clumped objects:Shape
-    Size of smoothing filter:0
-    Suppress local maxima that are closer than this minimum allowed distance:7
-    Speed up by using lower-resolution image to find local maxima?:Yes
-    Fill holes in identified objects?:After both thresholding and declumping
-    Automatically calculate size of smoothing filter for declumping?:Yes
-    Automatically calculate minimum allowed distance between local maxima?:Yes
-    Handling of objects if excessive number of objects identified:Continue
-    Maximum number of objects:500
-    Use advanced settings?:Yes
-    Threshold settings version:10
-    Threshold strategy:Global
-    Thresholding method:Otsu
-    Threshold smoothing scale:1.3488
-    Threshold correction factor:0.9
-    Lower and upper bounds on threshold:0.0,1.0
-    Manual threshold:0
-    Select the measurement to threshold with:None
-    Two-class or three-class thresholding?:Two classes
-    Assign pixels in the middle intensity class to the foreground or the background?:Foreground
-    Size of adaptive window:500
-    Lower outlier fraction:0.05
-    Upper outlier fraction:0.05
-    Averaging method:Mean
-    Variance method:Standard deviation
-    # of deviations:2.0
-    Thresholding method:Otsu
diff -r 3c3cd68d6d5a -r 27396311a314 test-data/identify_primary_objects_adv_adaptive_otsu.cppipe
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/identify_primary_objects_adv_adaptive_otsu.cppipe	Mon May 11 07:45:07 2020 -0400
@@ -0,0 +1,88 @@
+CellProfiler Pipeline: http://www.cellprofiler.org
+Version:3
+DateRevision:319
+GitHash:
+ModuleCount:5
+HasImagePlaneDetails:False
+
+Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    :
+    Filter images?:Images only
+    Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
+
+Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    Extract metadata?:Yes
+    Metadata data type:Text
+    Metadata types:{}
+    Extraction method count:1
+    Metadata extraction method:Extract from file/folder names
+    Metadata source:File name
+    Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)
+    Regular expression to extract from folder name:(?P<folderField1>.*)
+    Extract metadata from:All images
+    Select the filtering criteria:and (file does contain "")
+    Metadata file location:
+    Match file and image metadata:[]
+    Use case insensitive matching?:No
+
+NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Assign a name to:Images matching rules
+    Select the image type:Grayscale image
+    Name to assign these images:DNA
+    Match metadata:[]
+    Image set matching method:Order
+    Set intensity range from:Image metadata
+    Assignments count:1
+    Single images count:0
+    Maximum intensity:255.0
+    Process as 3D?:No
+    Relative pixel spacing in X:1.0
+    Relative pixel spacing in Y:1.0
+    Relative pixel spacing in Z:1.0
+    Select the rule criteria:and (file does startwith "im")
+    Name to assign these images:DNA
+    Name to assign these objects:Cell
+    Select the image type:Grayscale image
+    Set intensity range from:Image metadata
+    Select the image type:Grayscale image
+    Maximum intensity:255.0
+
+Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Do you want to group your images?:Yes
+    grouping metadata count:1
+    Metadata category:field1
+
+IdentifyPrimaryObjects:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:13|show_window:True|notes:\x5B\'Identify the nuclei from the DNA channel.\', \'PARAMS\x3A\', \'- Typical diameter of objects (Min,Max)\', \'- Method to distinguish clumped objects\x3A Shape/None. With Shape, the distance between the 2 centers can be changed.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Select the input image:DNA
+    Name the primary objects to be identified:Nuclei
+    Typical diameter of objects, in pixel units (Min,Max):15,200
+    Discard objects outside the diameter range?:Yes
+    Discard objects touching the border of the image?:Yes
+    Method to distinguish clumped objects:Shape
+    Method to draw dividing lines between clumped objects:Shape
+    Size of smoothing filter:1
+    Suppress local maxima that are closer than this minimum allowed distance:1
+    Speed up by using lower-resolution image to find local maxima?:Yes
+    Fill holes in identified objects?:After both thresholding and declumping
+    Automatically calculate size of smoothing filter for declumping?:No
+    Automatically calculate minimum allowed distance between local maxima?:No
+    Handling of objects if excessive number of objects identified:Continue
+    Maximum number of objects:500
+    Use advanced settings?:Yes
+    Threshold settings version:10
+    Threshold strategy:Adaptive
+    Thresholding method:Otsu
+    Threshold smoothing scale:1.5000
+    Threshold correction factor:1.0
+    Lower and upper bounds on threshold:0.0,1.0
+    Manual threshold:0
+    Select the measurement to threshold with:None
+    Two-class or three-class thresholding?:Three classes
+    Assign pixels in the middle intensity class to the foreground or the background?:Foreground
+    Size of adaptive window:50
+    Lower outlier fraction:0.05
+    Upper outlier fraction:0.05
+    Averaging method:Mean
+    Variance method:Standard deviation
+    # of deviations:2.00
+    Thresholding method:Otsu
diff -r 3c3cd68d6d5a -r 27396311a314 test-data/identify_primary_objects_adv_global_manual.cppipe
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/identify_primary_objects_adv_global_manual.cppipe	Mon May 11 07:45:07 2020 -0400
@@ -0,0 +1,88 @@
+CellProfiler Pipeline: http://www.cellprofiler.org
+Version:3
+DateRevision:319
+GitHash:
+ModuleCount:5
+HasImagePlaneDetails:False
+
+Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    :
+    Filter images?:Images only
+    Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
+
+Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    Extract metadata?:Yes
+    Metadata data type:Text
+    Metadata types:{}
+    Extraction method count:1
+    Metadata extraction method:Extract from file/folder names
+    Metadata source:File name
+    Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)
+    Regular expression to extract from folder name:(?P<folderField1>.*)
+    Extract metadata from:All images
+    Select the filtering criteria:and (file does contain "")
+    Metadata file location:
+    Match file and image metadata:[]
+    Use case insensitive matching?:No
+
+NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Assign a name to:Images matching rules
+    Select the image type:Grayscale image
+    Name to assign these images:DNA
+    Match metadata:[]
+    Image set matching method:Order
+    Set intensity range from:Image metadata
+    Assignments count:1
+    Single images count:0
+    Maximum intensity:255.0
+    Process as 3D?:No
+    Relative pixel spacing in X:1.0
+    Relative pixel spacing in Y:1.0
+    Relative pixel spacing in Z:1.0
+    Select the rule criteria:and (file does startwith "im")
+    Name to assign these images:DNA
+    Name to assign these objects:Cell
+    Select the image type:Grayscale image
+    Set intensity range from:Image metadata
+    Select the image type:Grayscale image
+    Maximum intensity:255.0
+
+Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Do you want to group your images?:Yes
+    grouping metadata count:1
+    Metadata category:field1
+
+IdentifyPrimaryObjects:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:13|show_window:True|notes:\x5B\'Identify the nuclei from the DNA channel.\', \'PARAMS\x3A\', \'- Typical diameter of objects (Min,Max)\', \'- Method to distinguish clumped objects\x3A Shape/None. With Shape, the distance between the 2 centers can be changed.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Select the input image:DNA
+    Name the primary objects to be identified:Nuclei
+    Typical diameter of objects, in pixel units (Min,Max):5,20
+    Discard objects outside the diameter range?:No
+    Discard objects touching the border of the image?:Yes
+    Method to distinguish clumped objects:Shape
+    Method to draw dividing lines between clumped objects:Shape
+    Size of smoothing filter:1
+    Suppress local maxima that are closer than this minimum allowed distance:1
+    Speed up by using lower-resolution image to find local maxima?:Yes
+    Fill holes in identified objects?:After both thresholding and declumping
+    Automatically calculate size of smoothing filter for declumping?:No
+    Automatically calculate minimum allowed distance between local maxima?:No
+    Handling of objects if excessive number of objects identified:Erase
+    Maximum number of objects:499
+    Use advanced settings?:Yes
+    Threshold settings version:10
+    Threshold strategy:Global
+    Thresholding method:Manual
+    Threshold smoothing scale:1.3488
+    Threshold correction factor:1.0
+    Lower and upper bounds on threshold:0.0,1.0
+    Manual threshold:1
+    Select the measurement to threshold with:None
+    Two-class or three-class thresholding?:Two classes
+    Assign pixels in the middle intensity class to the foreground or the background?:Foreground
+    Size of adaptive window:50
+    Lower outlier fraction:0.05
+    Upper outlier fraction:0.05
+    Averaging method:Mean
+    Variance method:Standard deviation
+    # of deviations:2.00
+    Thresholding method:Manual
diff -r 3c3cd68d6d5a -r 27396311a314 test-data/identify_primary_objects_adv_global_mce.cppipe
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/identify_primary_objects_adv_global_mce.cppipe	Mon May 11 07:45:07 2020 -0400
@@ -0,0 +1,88 @@
+CellProfiler Pipeline: http://www.cellprofiler.org
+Version:3
+DateRevision:319
+GitHash:
+ModuleCount:5
+HasImagePlaneDetails:False
+
+Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    :
+    Filter images?:Images only
+    Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
+
+Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    Extract metadata?:Yes
+    Metadata data type:Text
+    Metadata types:{}
+    Extraction method count:1
+    Metadata extraction method:Extract from file/folder names
+    Metadata source:File name
+    Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)
+    Regular expression to extract from folder name:(?P<folderField1>.*)
+    Extract metadata from:All images
+    Select the filtering criteria:and (file does contain "")
+    Metadata file location:
+    Match file and image metadata:[]
+    Use case insensitive matching?:No
+
+NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Assign a name to:Images matching rules
+    Select the image type:Grayscale image
+    Name to assign these images:DNA
+    Match metadata:[]
+    Image set matching method:Order
+    Set intensity range from:Image metadata
+    Assignments count:1
+    Single images count:0
+    Maximum intensity:255.0
+    Process as 3D?:No
+    Relative pixel spacing in X:1.0
+    Relative pixel spacing in Y:1.0
+    Relative pixel spacing in Z:1.0
+    Select the rule criteria:and (file does startwith "im")
+    Name to assign these images:DNA
+    Name to assign these objects:Cell
+    Select the image type:Grayscale image
+    Set intensity range from:Image metadata
+    Select the image type:Grayscale image
+    Maximum intensity:255.0
+
+Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Do you want to group your images?:Yes
+    grouping metadata count:1
+    Metadata category:field1
+
+IdentifyPrimaryObjects:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:13|show_window:True|notes:\x5B\'Identify the nuclei from the DNA channel.\', \'PARAMS\x3A\', \'- Typical diameter of objects (Min,Max)\', \'- Method to distinguish clumped objects\x3A Shape/None. With Shape, the distance between the 2 centers can be changed.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Select the input image:DNA
+    Name the primary objects to be identified:Nuclei
+    Typical diameter of objects, in pixel units (Min,Max):15,40
+    Discard objects outside the diameter range?:Yes
+    Discard objects touching the border of the image?:Yes
+    Method to distinguish clumped objects:Shape
+    Method to draw dividing lines between clumped objects:Shape
+    Size of smoothing filter:1
+    Suppress local maxima that are closer than this minimum allowed distance:7
+    Speed up by using lower-resolution image to find local maxima?:Yes
+    Fill holes in identified objects?:After both thresholding and declumping
+    Automatically calculate size of smoothing filter for declumping?:No
+    Automatically calculate minimum allowed distance between local maxima?:No
+    Handling of objects if excessive number of objects identified:Continue
+    Maximum number of objects:500
+    Use advanced settings?:Yes
+    Threshold settings version:10
+    Threshold strategy:Global
+    Thresholding method:Minimum cross entropy
+    Threshold smoothing scale:1.5000
+    Threshold correction factor:1.0
+    Lower and upper bounds on threshold:0.0,1.0
+    Manual threshold:0
+    Select the measurement to threshold with:None
+    Two-class or three-class thresholding?:Two classes
+    Assign pixels in the middle intensity class to the foreground or the background?:Foreground
+    Size of adaptive window:50
+    Lower outlier fraction:0.05
+    Upper outlier fraction:0.05
+    Averaging method:Mean
+    Variance method:Standard deviation
+    # of deviations:2.00
+    Thresholding method:Minimum cross entropy
diff -r 3c3cd68d6d5a -r 27396311a314 test-data/identify_primary_objects_adv_global_measurement.cppipe
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/identify_primary_objects_adv_global_measurement.cppipe	Mon May 11 07:45:07 2020 -0400
@@ -0,0 +1,88 @@
+CellProfiler Pipeline: http://www.cellprofiler.org
+Version:3
+DateRevision:319
+GitHash:
+ModuleCount:5
+HasImagePlaneDetails:False
+
+Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    :
+    Filter images?:Images only
+    Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
+
+Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    Extract metadata?:Yes
+    Metadata data type:Text
+    Metadata types:{}
+    Extraction method count:1
+    Metadata extraction method:Extract from file/folder names
+    Metadata source:File name
+    Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)
+    Regular expression to extract from folder name:(?P<folderField1>.*)
+    Extract metadata from:All images
+    Select the filtering criteria:and (file does contain "")
+    Metadata file location:
+    Match file and image metadata:[]
+    Use case insensitive matching?:No
+
+NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Assign a name to:Images matching rules
+    Select the image type:Grayscale image
+    Name to assign these images:DNA
+    Match metadata:[]
+    Image set matching method:Order
+    Set intensity range from:Image metadata
+    Assignments count:1
+    Single images count:0
+    Maximum intensity:255.0
+    Process as 3D?:No
+    Relative pixel spacing in X:1.0
+    Relative pixel spacing in Y:1.0
+    Relative pixel spacing in Z:1.0
+    Select the rule criteria:and (file does startwith "im")
+    Name to assign these images:DNA
+    Name to assign these objects:Cell
+    Select the image type:Grayscale image
+    Set intensity range from:Image metadata
+    Select the image type:Grayscale image
+    Maximum intensity:255.0
+
+Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Do you want to group your images?:Yes
+    grouping metadata count:1
+    Metadata category:field1
+
+IdentifyPrimaryObjects:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:13|show_window:True|notes:\x5B\'Identify the nuclei from the DNA channel.\', \'PARAMS\x3A\', \'- Typical diameter of objects (Min,Max)\', \'- Method to distinguish clumped objects\x3A Shape/None. With Shape, the distance between the 2 centers can be changed.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Select the input image:DNA
+    Name the primary objects to be identified:Nuclei
+    Typical diameter of objects, in pixel units (Min,Max):5,20
+    Discard objects outside the diameter range?:Yes
+    Discard objects touching the border of the image?:No
+    Method to distinguish clumped objects:Intensity
+    Method to draw dividing lines between clumped objects:Shape
+    Size of smoothing filter:0
+    Suppress local maxima that are closer than this minimum allowed distance:6
+    Speed up by using lower-resolution image to find local maxima?:Yes
+    Fill holes in identified objects?:After both thresholding and declumping
+    Automatically calculate size of smoothing filter for declumping?:Yes
+    Automatically calculate minimum allowed distance between local maxima?:No
+    Handling of objects if excessive number of objects identified:Continue
+    Maximum number of objects:500
+    Use advanced settings?:Yes
+    Threshold settings version:10
+    Threshold strategy:Global
+    Thresholding method:Measurement
+    Threshold smoothing scale:1.3488
+    Threshold correction factor:1.0
+    Lower and upper bounds on threshold:0.1,0.4
+    Manual threshold:0
+    Select the measurement to threshold with:FileName_DNA
+    Two-class or three-class thresholding?:Two classes
+    Assign pixels in the middle intensity class to the foreground or the background?:Foreground
+    Size of adaptive window:50
+    Lower outlier fraction:0.05
+    Upper outlier fraction:0.05
+    Averaging method:Mean
+    Variance method:Standard deviation
+    # of deviations:2.00
+    Thresholding method:Measurement
diff -r 3c3cd68d6d5a -r 27396311a314 test-data/identify_primary_objects_adv_global_rb.cppipe
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/identify_primary_objects_adv_global_rb.cppipe	Mon May 11 07:45:07 2020 -0400
@@ -0,0 +1,88 @@
+CellProfiler Pipeline: http://www.cellprofiler.org
+Version:3
+DateRevision:319
+GitHash:
+ModuleCount:5
+HasImagePlaneDetails:False
+
+Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    :
+    Filter images?:Images only
+    Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
+
+Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    Extract metadata?:Yes
+    Metadata data type:Text
+    Metadata types:{}
+    Extraction method count:1
+    Metadata extraction method:Extract from file/folder names
+    Metadata source:File name
+    Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)
+    Regular expression to extract from folder name:(?P<folderField1>.*)
+    Extract metadata from:All images
+    Select the filtering criteria:and (file does contain "")
+    Metadata file location:
+    Match file and image metadata:[]
+    Use case insensitive matching?:No
+
+NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Assign a name to:Images matching rules
+    Select the image type:Grayscale image
+    Name to assign these images:DNA
+    Match metadata:[]
+    Image set matching method:Order
+    Set intensity range from:Image metadata
+    Assignments count:1
+    Single images count:0
+    Maximum intensity:255.0
+    Process as 3D?:No
+    Relative pixel spacing in X:1.0
+    Relative pixel spacing in Y:1.0
+    Relative pixel spacing in Z:1.0
+    Select the rule criteria:and (file does startwith "im")
+    Name to assign these images:DNA
+    Name to assign these objects:Cell
+    Select the image type:Grayscale image
+    Set intensity range from:Image metadata
+    Select the image type:Grayscale image
+    Maximum intensity:255.0
+
+Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Do you want to group your images?:Yes
+    grouping metadata count:1
+    Metadata category:field1
+
+IdentifyPrimaryObjects:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:13|show_window:True|notes:\x5B\'Identify the nuclei from the DNA channel.\', \'PARAMS\x3A\', \'- Typical diameter of objects (Min,Max)\', \'- Method to distinguish clumped objects\x3A Shape/None. With Shape, the distance between the 2 centers can be changed.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Select the input image:DNA
+    Name the primary objects to be identified:Nuclei
+    Typical diameter of objects, in pixel units (Min,Max):10,40
+    Discard objects outside the diameter range?:Yes
+    Discard objects touching the border of the image?:Yes
+    Method to distinguish clumped objects:Shape
+    Method to draw dividing lines between clumped objects:Shape
+    Size of smoothing filter:1
+    Suppress local maxima that are closer than this minimum allowed distance:7
+    Speed up by using lower-resolution image to find local maxima?:Yes
+    Fill holes in identified objects?:After both thresholding and declumping
+    Automatically calculate size of smoothing filter for declumping?:No
+    Automatically calculate minimum allowed distance between local maxima?:No
+    Handling of objects if excessive number of objects identified:Continue
+    Maximum number of objects:500
+    Use advanced settings?:Yes
+    Threshold settings version:10
+    Threshold strategy:Global
+    Thresholding method:RobustBackground
+    Threshold smoothing scale:1.4000
+    Threshold correction factor:1.0
+    Lower and upper bounds on threshold:0.0,1.0
+    Manual threshold:0
+    Select the measurement to threshold with:None
+    Two-class or three-class thresholding?:Two classes
+    Assign pixels in the middle intensity class to the foreground or the background?:Foreground
+    Size of adaptive window:50
+    Lower outlier fraction:0.06
+    Upper outlier fraction:0.07
+    Averaging method:Median
+    Variance method:Median absolute deviation
+    # of deviations:3.00
+    Thresholding method:RobustBackground
diff -r 3c3cd68d6d5a -r 27396311a314 test-data/identify_primary_objects_noadv.cppipe
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/identify_primary_objects_noadv.cppipe	Mon May 11 07:45:07 2020 -0400
@@ -0,0 +1,88 @@
+CellProfiler Pipeline: http://www.cellprofiler.org
+Version:3
+DateRevision:319
+GitHash:
+ModuleCount:5
+HasImagePlaneDetails:False
+
+Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    :
+    Filter images?:Images only
+    Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
+
+Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    Extract metadata?:Yes
+    Metadata data type:Text
+    Metadata types:{}
+    Extraction method count:1
+    Metadata extraction method:Extract from file/folder names
+    Metadata source:File name
+    Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)
+    Regular expression to extract from folder name:(?P<folderField1>.*)
+    Extract metadata from:All images
+    Select the filtering criteria:and (file does contain "")
+    Metadata file location:
+    Match file and image metadata:[]
+    Use case insensitive matching?:No
+
+NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Assign a name to:Images matching rules
+    Select the image type:Grayscale image
+    Name to assign these images:DNA
+    Match metadata:[]
+    Image set matching method:Order
+    Set intensity range from:Image metadata
+    Assignments count:1
+    Single images count:0
+    Maximum intensity:255.0
+    Process as 3D?:No
+    Relative pixel spacing in X:1.0
+    Relative pixel spacing in Y:1.0
+    Relative pixel spacing in Z:1.0
+    Select the rule criteria:and (file does startwith "im")
+    Name to assign these images:DNA
+    Name to assign these objects:Cell
+    Select the image type:Grayscale image
+    Set intensity range from:Image metadata
+    Select the image type:Grayscale image
+    Maximum intensity:255.0
+
+Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Do you want to group your images?:Yes
+    grouping metadata count:1
+    Metadata category:field1
+
+IdentifyPrimaryObjects:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:13|show_window:True|notes:\x5B\'Identify the nuclei from the DNA channel.\', \'PARAMS\x3A\', \'- Typical diameter of objects (Min,Max)\', \'- Method to distinguish clumped objects\x3A Shape/None. With Shape, the distance between the 2 centers can be changed.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Select the input image:DNA
+    Name the primary objects to be identified:Nuclei
+    Typical diameter of objects, in pixel units (Min,Max):15,200
+    Discard objects outside the diameter range?:Yes
+    Discard objects touching the border of the image?:Yes
+    Method to distinguish clumped objects:Intensity
+    Method to draw dividing lines between clumped objects:Intensity
+    Size of smoothing filter:1
+    Suppress local maxima that are closer than this minimum allowed distance:7
+    Speed up by using lower-resolution image to find local maxima?:Yes
+    Fill holes in identified objects?:After both thresholding and declumping
+    Automatically calculate size of smoothing filter for declumping?:Yes
+    Automatically calculate minimum allowed distance between local maxima?:Yes
+    Handling of objects if excessive number of objects identified:Continue
+    Maximum number of objects:500
+    Use advanced settings?:No
+    Threshold settings version:10
+    Threshold strategy:Global
+    Thresholding method:Minimum cross entropy
+    Threshold smoothing scale:1.3488
+    Threshold correction factor:1.0
+    Lower and upper bounds on threshold:0.0,1.0
+    Manual threshold:0
+    Select the measurement to threshold with:None
+    Two-class or three-class thresholding?:Two classes
+    Assign pixels in the middle intensity class to the foreground or the background?:Foreground
+    Size of adaptive window:50
+    Lower outlier fraction:0.05
+    Upper outlier fraction:0.05
+    Averaging method:Mean
+    Variance method:Standard deviation
+    # of deviations:2.00
+    Thresholding method:Minimum cross entropy
diff -r 3c3cd68d6d5a -r 27396311a314 test-data/image_math.xml
diff -r 3c3cd68d6d5a -r 27396311a314 test-data/images.tar
Binary file test-data/images.tar has changed
diff -r 3c3cd68d6d5a -r 27396311a314 test-data/mask_image.cppipe
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/mask_image.cppipe	Mon May 11 07:45:07 2020 -0400
@@ -0,0 +1,61 @@
+CellProfiler Pipeline: http://www.cellprofiler.org
+Version:3
+DateRevision:319
+GitHash:
+ModuleCount:5
+HasImagePlaneDetails:False
+
+Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    :
+    Filter images?:Images only
+    Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
+
+Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    Extract metadata?:Yes
+    Metadata data type:Text
+    Metadata types:{}
+    Extraction method count:1
+    Metadata extraction method:Extract from file/folder names
+    Metadata source:File name
+    Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)
+    Regular expression to extract from folder name:(?P<folderField1>.*)
+    Extract metadata from:All images
+    Select the filtering criteria:and (file does contain "")
+    Metadata file location:
+    Match file and image metadata:[]
+    Use case insensitive matching?:No
+
+NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Assign a name to:Images matching rules
+    Select the image type:Grayscale image
+    Name to assign these images:DNA
+    Match metadata:[]
+    Image set matching method:Order
+    Set intensity range from:Image metadata
+    Assignments count:1
+    Single images count:0
+    Maximum intensity:255.0
+    Process as 3D?:No
+    Relative pixel spacing in X:1.0
+    Relative pixel spacing in Y:1.0
+    Relative pixel spacing in Z:1.0
+    Select the rule criteria:and (file does startwith "im")
+    Name to assign these images:DNA
+    Name to assign these objects:Cell
+    Select the image type:Grayscale image
+    Set intensity range from:Image metadata
+    Select the image type:Grayscale image
+    Maximum intensity:255.0
+
+Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Do you want to group your images?:Yes
+    grouping metadata count:1
+    Metadata category:field1
+
+MaskImage:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:3|show_window:False|notes:\x5B'Keep only nucleoli inside the nuclei\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Select the input image:DNAdarkholes
+    Name the output image:MaskDNAdarkholes
+    Use objects or an image as a mask?:Objects
+    Select object for mask:Nuclei
+    Select image for mask:None
+    Invert the mask?:No
diff -r 3c3cd68d6d5a -r 27396311a314 test-data/mask_image.txt
--- a/test-data/mask_image.txt	Thu Apr 16 05:29:02 2020 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,61 +0,0 @@
-CellProfiler Pipeline: http://www.cellprofiler.org
-Version:3
-DateRevision:319
-GitHash:
-ModuleCount:5
-HasImagePlaneDetails:False
-
-Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
-    :
-    Filter images?:Images only
-    Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
-
-Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
-    Extract metadata?:Yes
-    Metadata data type:Text
-    Metadata types:{}
-    Extraction method count:1
-    Metadata extraction method:Extract from file/folder names
-    Metadata source:File name
-    Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)
-    Regular expression to extract from folder name:(?P<field1>.*)
-    Extract metadata from:All images
-    Select the filtering criteria:and (file does contain "")
-    Metadata file location:
-    Match file and image metadata:[]
-    Use case insensitive matching?:No
-
-NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
-    Assign a name to:Images matching rules
-    Select the image type:Grayscale image
-    Name to assign these images:DNA
-    Match metadata:[]
-    Image set matching method:Order
-    Set intensity range from:Image metadata
-    Assignments count:1
-    Single images count:0
-    Maximum intensity:255.0
-    Process as 3D?:No
-    Relative pixel spacing in X:1.0
-    Relative pixel spacing in Y:1.0
-    Relative pixel spacing in Z:1.0
-    Select the rule criteria:and (file does startwith "im")
-    Name to assign these images:DNA
-    Name to assign these objects:Cell
-    Select the image type:Grayscale image
-    Set intensity range from:Image metadata
-    Select the image type:Grayscale image
-    Maximum intensity:255.0
-
-Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
-    Do you want to group your images?:Yes
-    grouping metadata count:1
-    Metadata category:Screen
-
-MaskImage:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:3|show_window:False|notes:\x5B'Keep only nucleoli inside the nuclei\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
-    Select the input image:DNAdarkholes
-    Name the output image:MaskDNAdarkholes
-    Use objects or an image as a mask?:Objects
-    Select object for mask:Nuclei
-    Select image for mask:None
-    Invert the mask?:No
diff -r 3c3cd68d6d5a -r 27396311a314 test-data/measure_granularity.cppipe
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/measure_granularity.cppipe	Mon May 11 07:45:07 2020 -0400
@@ -0,0 +1,62 @@
+CellProfiler Pipeline: http://www.cellprofiler.org
+Version:3
+DateRevision:319
+GitHash:
+ModuleCount:5
+HasImagePlaneDetails:False
+
+Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    :
+    Filter images?:Images only
+    Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
+
+Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    Extract metadata?:Yes
+    Metadata data type:Text
+    Metadata types:{}
+    Extraction method count:1
+    Metadata extraction method:Extract from file/folder names
+    Metadata source:File name
+    Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)
+    Regular expression to extract from folder name:(?P<folderField1>.*)
+    Extract metadata from:All images
+    Select the filtering criteria:and (file does contain "")
+    Metadata file location:
+    Match file and image metadata:[]
+    Use case insensitive matching?:No
+
+NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Assign a name to:Images matching rules
+    Select the image type:Grayscale image
+    Name to assign these images:DNA
+    Match metadata:[]
+    Image set matching method:Order
+    Set intensity range from:Image metadata
+    Assignments count:1
+    Single images count:0
+    Maximum intensity:255.0
+    Process as 3D?:No
+    Relative pixel spacing in X:1.0
+    Relative pixel spacing in Y:1.0
+    Relative pixel spacing in Z:1.0
+    Select the rule criteria:and (file does startwith "im")
+    Name to assign these images:DNA
+    Name to assign these objects:Cell
+    Select the image type:Grayscale image
+    Set intensity range from:Image metadata
+    Select the image type:Grayscale image
+    Maximum intensity:255.0
+
+Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Do you want to group your images?:Yes
+    grouping metadata count:1
+    Metadata category:field1
+
+MeasureGranularity:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:3|show_window:False|notes:\x5B\'PARAMS\x3A\', \'- Radius\', '- Range\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Image count:1
+    Object count:0
+    Select an image to measure:DNA
+    Subsampling factor for granularity measurements:0.25
+    Subsampling factor for background reduction:0.25
+    Radius of structuring element:10
+    Range of the granular spectrum:16
diff -r 3c3cd68d6d5a -r 27396311a314 test-data/measure_granularity.txt
--- a/test-data/measure_granularity.txt	Thu Apr 16 05:29:02 2020 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,62 +0,0 @@
-CellProfiler Pipeline: http://www.cellprofiler.org
-Version:3
-DateRevision:319
-GitHash:
-ModuleCount:5
-HasImagePlaneDetails:False
-
-Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
-    :
-    Filter images?:Images only
-    Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
-
-Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
-    Extract metadata?:Yes
-    Metadata data type:Text
-    Metadata types:{}
-    Extraction method count:1
-    Metadata extraction method:Extract from file/folder names
-    Metadata source:File name
-    Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)
-    Regular expression to extract from folder name:(?P<field1>.*)
-    Extract metadata from:All images
-    Select the filtering criteria:and (file does contain "")
-    Metadata file location:
-    Match file and image metadata:[]
-    Use case insensitive matching?:No
-
-NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
-    Assign a name to:Images matching rules
-    Select the image type:Grayscale image
-    Name to assign these images:DNA
-    Match metadata:[]
-    Image set matching method:Order
-    Set intensity range from:Image metadata
-    Assignments count:1
-    Single images count:0
-    Maximum intensity:255.0
-    Process as 3D?:No
-    Relative pixel spacing in X:1.0
-    Relative pixel spacing in Y:1.0
-    Relative pixel spacing in Z:1.0
-    Select the rule criteria:and (file does startwith "im")
-    Name to assign these images:DNA
-    Name to assign these objects:Cell
-    Select the image type:Grayscale image
-    Set intensity range from:Image metadata
-    Select the image type:Grayscale image
-    Maximum intensity:255.0
-
-Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
-    Do you want to group your images?:Yes
-    grouping metadata count:1
-    Metadata category:Screen
-
-MeasureGranularity:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:3|show_window:False|notes:\x5B\'PARAMS\x3A\', \'- Radius\', '- Range\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
-    Image count:1
-    Object count:0
-    Select an image to measure:DNA
-    Subsampling factor for granularity measurements:0.25
-    Subsampling factor for background reduction:0.25
-    Radius of structuring element:10
-    Range of the granular spectrum:16
diff -r 3c3cd68d6d5a -r 27396311a314 test-data/measure_image_area_occupied.cppipe
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/measure_image_area_occupied.cppipe	Mon May 11 07:45:07 2020 -0400
@@ -0,0 +1,62 @@
+CellProfiler Pipeline: http://www.cellprofiler.org
+Version:3
+DateRevision:319
+GitHash:
+ModuleCount:5
+HasImagePlaneDetails:False
+
+Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    :
+    Filter images?:Images only
+    Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
+
+Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    Extract metadata?:Yes
+    Metadata data type:Text
+    Metadata types:{}
+    Extraction method count:1
+    Metadata extraction method:Extract from file/folder names
+    Metadata source:File name
+    Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)
+    Regular expression to extract from folder name:(?P<folderField1>.*)
+    Extract metadata from:All images
+    Select the filtering criteria:and (file does contain "")
+    Metadata file location:
+    Match file and image metadata:[]
+    Use case insensitive matching?:No
+
+NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Assign a name to:Images matching rules
+    Select the image type:Grayscale image
+    Name to assign these images:DNA
+    Match metadata:[]
+    Image set matching method:Order
+    Set intensity range from:Image metadata
+    Assignments count:1
+    Single images count:0
+    Maximum intensity:255.0
+    Process as 3D?:No
+    Relative pixel spacing in X:1.0
+    Relative pixel spacing in Y:1.0
+    Relative pixel spacing in Z:1.0
+    Select the rule criteria:and (file does startwith "im")
+    Name to assign these images:DNA
+    Name to assign these objects:Cell
+    Select the image type:Grayscale image
+    Set intensity range from:Image metadata
+    Select the image type:Grayscale image
+    Maximum intensity:255.0
+
+Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Do you want to group your images?:Yes
+    grouping metadata count:1
+    Metadata category:field1
+
+MeasureImageAreaOccupied:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Hidden:2
+    Measure the area occupied in a binary image, or in objects?:Objects
+    Select objects to measure:Nuclei
+    Select a binary image to measure:None
+    Measure the area occupied in a binary image, or in objects?:Objects
+    Select objects to measure:Nucleoli
+    Select a binary image to measure:None
diff -r 3c3cd68d6d5a -r 27396311a314 test-data/measure_image_area_occupied.txt
--- a/test-data/measure_image_area_occupied.txt	Thu Apr 16 05:29:02 2020 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,62 +0,0 @@
-CellProfiler Pipeline: http://www.cellprofiler.org
-Version:3
-DateRevision:319
-GitHash:
-ModuleCount:5
-HasImagePlaneDetails:False
-
-Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
-    :
-    Filter images?:Images only
-    Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
-
-Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
-    Extract metadata?:Yes
-    Metadata data type:Text
-    Metadata types:{}
-    Extraction method count:1
-    Metadata extraction method:Extract from file/folder names
-    Metadata source:File name
-    Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)
-    Regular expression to extract from folder name:(?P<field1>.*)
-    Extract metadata from:All images
-    Select the filtering criteria:and (file does contain "")
-    Metadata file location:
-    Match file and image metadata:[]
-    Use case insensitive matching?:No
-
-NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
-    Assign a name to:Images matching rules
-    Select the image type:Grayscale image
-    Name to assign these images:DNA
-    Match metadata:[]
-    Image set matching method:Order
-    Set intensity range from:Image metadata
-    Assignments count:1
-    Single images count:0
-    Maximum intensity:255.0
-    Process as 3D?:No
-    Relative pixel spacing in X:1.0
-    Relative pixel spacing in Y:1.0
-    Relative pixel spacing in Z:1.0
-    Select the rule criteria:and (file does startwith "im")
-    Name to assign these images:DNA
-    Name to assign these objects:Cell
-    Select the image type:Grayscale image
-    Set intensity range from:Image metadata
-    Select the image type:Grayscale image
-    Maximum intensity:255.0
-
-Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
-    Do you want to group your images?:Yes
-    grouping metadata count:1
-    Metadata category:Screen
-
-MeasureImageAreaOccupied:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
-    Hidden:2
-    Measure the area occupied in a binary image, or in objects?:Objects
-    Select objects to measure:Nuclei
-    Select a binary image to measure:None
-    Measure the area occupied in a binary image, or in objects?:Objects
-    Select objects to measure:Nucleoli
-    Select a binary image to measure:None
diff -r 3c3cd68d6d5a -r 27396311a314 test-data/measure_image_intensity.cppipe
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/measure_image_intensity.cppipe	Mon May 11 07:45:07 2020 -0400
@@ -0,0 +1,61 @@
+CellProfiler Pipeline: http://www.cellprofiler.org
+Version:3
+DateRevision:319
+GitHash:
+ModuleCount:5
+HasImagePlaneDetails:False
+
+Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    :
+    Filter images?:Images only
+    Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
+
+Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    Extract metadata?:Yes
+    Metadata data type:Text
+    Metadata types:{}
+    Extraction method count:1
+    Metadata extraction method:Extract from file/folder names
+    Metadata source:File name
+    Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)
+    Regular expression to extract from folder name:(?P<folderField1>.*)
+    Extract metadata from:All images
+    Select the filtering criteria:and (file does contain "")
+    Metadata file location:
+    Match file and image metadata:[]
+    Use case insensitive matching?:No
+
+NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Assign a name to:Images matching rules
+    Select the image type:Grayscale image
+    Name to assign these images:DNA
+    Match metadata:[]
+    Image set matching method:Order
+    Set intensity range from:Image metadata
+    Assignments count:1
+    Single images count:0
+    Maximum intensity:255.0
+    Process as 3D?:No
+    Relative pixel spacing in X:1.0
+    Relative pixel spacing in Y:1.0
+    Relative pixel spacing in Z:1.0
+    Select the rule criteria:and (file does startwith "im")
+    Name to assign these images:DNA
+    Name to assign these objects:Cell
+    Select the image type:Grayscale image
+    Set intensity range from:Image metadata
+    Select the image type:Grayscale image
+    Maximum intensity:255.0
+
+Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Do you want to group your images?:Yes
+    grouping metadata count:1
+    Metadata category:field1
+
+MeasureImageIntensity:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Select the image to measure:DNA
+    Measure the intensity only from areas enclosed by objects?:No
+    Select the input objects:None
+    Select the image to measure:DNA
+    Measure the intensity only from areas enclosed by objects?:Yes
+    Select the input objects:Nuclei
diff -r 3c3cd68d6d5a -r 27396311a314 test-data/measure_image_intensity.txt
--- a/test-data/measure_image_intensity.txt	Thu Apr 16 05:29:02 2020 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,61 +0,0 @@
-CellProfiler Pipeline: http://www.cellprofiler.org
-Version:3
-DateRevision:319
-GitHash:
-ModuleCount:5
-HasImagePlaneDetails:False
-
-Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
-    :
-    Filter images?:Images only
-    Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
-
-Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
-    Extract metadata?:Yes
-    Metadata data type:Text
-    Metadata types:{}
-    Extraction method count:1
-    Metadata extraction method:Extract from file/folder names
-    Metadata source:File name
-    Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)
-    Regular expression to extract from folder name:(?P<field1>.*)
-    Extract metadata from:All images
-    Select the filtering criteria:and (file does contain "")
-    Metadata file location:
-    Match file and image metadata:[]
-    Use case insensitive matching?:No
-
-NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
-    Assign a name to:Images matching rules
-    Select the image type:Grayscale image
-    Name to assign these images:DNA
-    Match metadata:[]
-    Image set matching method:Order
-    Set intensity range from:Image metadata
-    Assignments count:1
-    Single images count:0
-    Maximum intensity:255.0
-    Process as 3D?:No
-    Relative pixel spacing in X:1.0
-    Relative pixel spacing in Y:1.0
-    Relative pixel spacing in Z:1.0
-    Select the rule criteria:and (file does startwith "im")
-    Name to assign these images:DNA
-    Name to assign these objects:Cell
-    Select the image type:Grayscale image
-    Set intensity range from:Image metadata
-    Select the image type:Grayscale image
-    Maximum intensity:255.0
-
-Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
-    Do you want to group your images?:Yes
-    grouping metadata count:1
-    Metadata category:Screen
-
-MeasureImageIntensity:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
-    Select the image to measure:DNA
-    Measure the intensity only from areas enclosed by objects?:No
-    Select the input objects:None
-    Select the image to measure:DNA
-    Measure the intensity only from areas enclosed by objects?:Yes
-    Select the input objects:Nuclei
diff -r 3c3cd68d6d5a -r 27396311a314 test-data/measure_image_quality.cppipe
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/measure_image_quality.cppipe	Mon May 11 07:45:07 2020 -0400
@@ -0,0 +1,72 @@
+CellProfiler Pipeline: http://www.cellprofiler.org
+Version:3
+DateRevision:319
+GitHash:
+ModuleCount:5
+HasImagePlaneDetails:False
+
+Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    :
+    Filter images?:Images only
+    Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
+
+Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    Extract metadata?:Yes
+    Metadata data type:Text
+    Metadata types:{}
+    Extraction method count:1
+    Metadata extraction method:Extract from file/folder names
+    Metadata source:File name
+    Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)
+    Regular expression to extract from folder name:(?P<folderField1>.*)
+    Extract metadata from:All images
+    Select the filtering criteria:and (file does contain "")
+    Metadata file location:
+    Match file and image metadata:[]
+    Use case insensitive matching?:No
+
+NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Assign a name to:Images matching rules
+    Select the image type:Grayscale image
+    Name to assign these images:DNA
+    Match metadata:[]
+    Image set matching method:Order
+    Set intensity range from:Image metadata
+    Assignments count:1
+    Single images count:0
+    Maximum intensity:255.0
+    Process as 3D?:No
+    Relative pixel spacing in X:1.0
+    Relative pixel spacing in Y:1.0
+    Relative pixel spacing in Z:1.0
+    Select the rule criteria:and (file does startwith "im")
+    Name to assign these images:DNA
+    Name to assign these objects:Cell
+    Select the image type:Grayscale image
+    Set intensity range from:Image metadata
+    Select the image type:Grayscale image
+    Maximum intensity:255.0
+
+Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Do you want to group your images?:Yes
+    grouping metadata count:1
+    Metadata category:field1
+
+MeasureImageQuality:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:5|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Calculate metrics for which images?:All loaded images
+    Image count:1
+    Scale count:1
+    Threshold count:1
+    Select the images to measure:
+    Include the image rescaling value?:Yes
+    Calculate blur metrics?:Yes
+    Spatial scale for blur measurements:20
+    Calculate saturation metrics?:Yes
+    Calculate intensity metrics?:Yes
+    Calculate thresholds?:Yes
+    Use all thresholding methods?:No
+    Select a thresholding method:Otsu
+    Typical fraction of the image covered by objects:0.1
+    Two-class or three-class thresholding?:Two classes
+    Minimize the weighted variance or the entropy:Weighted variance
+    Assign pixels in the middle intensity class to the foreground or the background?:Foreground
diff -r 3c3cd68d6d5a -r 27396311a314 test-data/measure_image_quality.txt
--- a/test-data/measure_image_quality.txt	Thu Apr 16 05:29:02 2020 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,72 +0,0 @@
-CellProfiler Pipeline: http://www.cellprofiler.org
-Version:3
-DateRevision:319
-GitHash:
-ModuleCount:5
-HasImagePlaneDetails:False
-
-Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
-    :
-    Filter images?:Images only
-    Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
-
-Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
-    Extract metadata?:Yes
-    Metadata data type:Text
-    Metadata types:{}
-    Extraction method count:1
-    Metadata extraction method:Extract from file/folder names
-    Metadata source:File name
-    Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)
-    Regular expression to extract from folder name:(?P<field1>.*)
-    Extract metadata from:All images
-    Select the filtering criteria:and (file does contain "")
-    Metadata file location:
-    Match file and image metadata:[]
-    Use case insensitive matching?:No
-
-NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
-    Assign a name to:Images matching rules
-    Select the image type:Grayscale image
-    Name to assign these images:DNA
-    Match metadata:[]
-    Image set matching method:Order
-    Set intensity range from:Image metadata
-    Assignments count:1
-    Single images count:0
-    Maximum intensity:255.0
-    Process as 3D?:No
-    Relative pixel spacing in X:1.0
-    Relative pixel spacing in Y:1.0
-    Relative pixel spacing in Z:1.0
-    Select the rule criteria:and (file does startwith "im")
-    Name to assign these images:DNA
-    Name to assign these objects:Cell
-    Select the image type:Grayscale image
-    Set intensity range from:Image metadata
-    Select the image type:Grayscale image
-    Maximum intensity:255.0
-
-Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
-    Do you want to group your images?:Yes
-    grouping metadata count:1
-    Metadata category:Screen
-
-MeasureImageQuality:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:5|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
-    Calculate metrics for which images?:All loaded images
-    Image count:1
-    Scale count:1
-    Threshold count:1
-    Select the images to measure:
-    Include the image rescaling value?:Yes
-    Calculate blur metrics?:Yes
-    Spatial scale for blur measurements:20
-    Calculate saturation metrics?:Yes
-    Calculate intensity metrics?:Yes
-    Calculate thresholds?:Yes
-    Use all thresholding methods?:No
-    Select a thresholding method:Otsu
-    Typical fraction of the image covered by objects:0.1
-    Two-class or three-class thresholding?:Two classes
-    Minimize the weighted variance or the entropy:Weighted variance
-    Assign pixels in the middle intensity class to the foreground or the background?:Foreground
diff -r 3c3cd68d6d5a -r 27396311a314 test-data/measure_object_intensity.cppipe
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/measure_object_intensity.cppipe	Mon May 11 07:45:07 2020 -0400
@@ -0,0 +1,58 @@
+CellProfiler Pipeline: http://www.cellprofiler.org
+Version:3
+DateRevision:319
+GitHash:
+ModuleCount:5
+HasImagePlaneDetails:False
+
+Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    :
+    Filter images?:Images only
+    Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
+
+Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    Extract metadata?:Yes
+    Metadata data type:Text
+    Metadata types:{}
+    Extraction method count:1
+    Metadata extraction method:Extract from file/folder names
+    Metadata source:File name
+    Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)
+    Regular expression to extract from folder name:(?P<folderField1>.*)
+    Extract metadata from:All images
+    Select the filtering criteria:and (file does contain "")
+    Metadata file location:
+    Match file and image metadata:[]
+    Use case insensitive matching?:No
+
+NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Assign a name to:Images matching rules
+    Select the image type:Grayscale image
+    Name to assign these images:DNA
+    Match metadata:[]
+    Image set matching method:Order
+    Set intensity range from:Image metadata
+    Assignments count:1
+    Single images count:0
+    Maximum intensity:255.0
+    Process as 3D?:No
+    Relative pixel spacing in X:1.0
+    Relative pixel spacing in Y:1.0
+    Relative pixel spacing in Z:1.0
+    Select the rule criteria:and (file does startwith "im")
+    Name to assign these images:DNA
+    Name to assign these objects:Cell
+    Select the image type:Grayscale image
+    Set intensity range from:Image metadata
+    Select the image type:Grayscale image
+    Maximum intensity:255.0
+
+Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Do you want to group your images?:Yes
+    grouping metadata count:1
+    Metadata category:field1
+
+MeasureObjectIntensity:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:3|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Hidden:1
+    Select an image to measure:DNA
+    Select objects to measure:Nuclei
diff -r 3c3cd68d6d5a -r 27396311a314 test-data/measure_object_intensity.txt
--- a/test-data/measure_object_intensity.txt	Thu Apr 16 05:29:02 2020 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,58 +0,0 @@
-CellProfiler Pipeline: http://www.cellprofiler.org
-Version:3
-DateRevision:319
-GitHash:
-ModuleCount:5
-HasImagePlaneDetails:False
-
-Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
-    :
-    Filter images?:Images only
-    Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
-
-Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
-    Extract metadata?:Yes
-    Metadata data type:Text
-    Metadata types:{}
-    Extraction method count:1
-    Metadata extraction method:Extract from file/folder names
-    Metadata source:File name
-    Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)
-    Regular expression to extract from folder name:(?P<field1>.*)
-    Extract metadata from:All images
-    Select the filtering criteria:and (file does contain "")
-    Metadata file location:
-    Match file and image metadata:[]
-    Use case insensitive matching?:No
-
-NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
-    Assign a name to:Images matching rules
-    Select the image type:Grayscale image
-    Name to assign these images:DNA
-    Match metadata:[]
-    Image set matching method:Order
-    Set intensity range from:Image metadata
-    Assignments count:1
-    Single images count:0
-    Maximum intensity:255.0
-    Process as 3D?:No
-    Relative pixel spacing in X:1.0
-    Relative pixel spacing in Y:1.0
-    Relative pixel spacing in Z:1.0
-    Select the rule criteria:and (file does startwith "im")
-    Name to assign these images:DNA
-    Name to assign these objects:Cell
-    Select the image type:Grayscale image
-    Set intensity range from:Image metadata
-    Select the image type:Grayscale image
-    Maximum intensity:255.0
-
-Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
-    Do you want to group your images?:Yes
-    grouping metadata count:1
-    Metadata category:Screen
-
-MeasureObjectIntensity:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:3|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
-    Hidden:1
-    Select an image to measure:DNA
-    Select objects to measure:Nuclei
diff -r 3c3cd68d6d5a -r 27396311a314 test-data/measure_object_size.txt
diff -r 3c3cd68d6d5a -r 27396311a314 test-data/measure_object_size_shape.cppipe
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/measure_object_size_shape.cppipe	Mon May 11 07:45:07 2020 -0400
@@ -0,0 +1,58 @@
+CellProfiler Pipeline: http://www.cellprofiler.org
+Version:3
+DateRevision:319
+GitHash:
+ModuleCount:5
+HasImagePlaneDetails:False
+
+Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    :
+    Filter images?:Images only
+    Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
+
+Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    Extract metadata?:Yes
+    Metadata data type:Text
+    Metadata types:{}
+    Extraction method count:1
+    Metadata extraction method:Extract from file/folder names
+    Metadata source:File name
+    Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)
+    Regular expression to extract from folder name:(?P<folderField1>.*)
+    Extract metadata from:All images
+    Select the filtering criteria:and (file does contain "")
+    Metadata file location:
+    Match file and image metadata:[]
+    Use case insensitive matching?:No
+
+NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Assign a name to:Images matching rules
+    Select the image type:Grayscale image
+    Name to assign these images:DNA
+    Match metadata:[]
+    Image set matching method:Order
+    Set intensity range from:Image metadata
+    Assignments count:1
+    Single images count:0
+    Maximum intensity:255.0
+    Process as 3D?:No
+    Relative pixel spacing in X:1.0
+    Relative pixel spacing in Y:1.0
+    Relative pixel spacing in Z:1.0
+    Select the rule criteria:and (file does startwith "im")
+    Name to assign these images:DNA
+    Name to assign these objects:Cell
+    Select the image type:Grayscale image
+    Set intensity range from:Image metadata
+    Select the image type:Grayscale image
+    Maximum intensity:255.0
+
+Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Do you want to group your images?:Yes
+    grouping metadata count:1
+    Metadata category:field1
+
+MeasureObjectSizeShape:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:1|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Select objects to measure:Nuclei
+    Select objects to measure:Nucleoli
+    Calculate the Zernike features?:Yes
diff -r 3c3cd68d6d5a -r 27396311a314 test-data/measure_object_size_shape.txt
--- a/test-data/measure_object_size_shape.txt	Thu Apr 16 05:29:02 2020 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,58 +0,0 @@
-CellProfiler Pipeline: http://www.cellprofiler.org
-Version:3
-DateRevision:319
-GitHash:
-ModuleCount:5
-HasImagePlaneDetails:False
-
-Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
-    :
-    Filter images?:Images only
-    Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
-
-Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
-    Extract metadata?:Yes
-    Metadata data type:Text
-    Metadata types:{}
-    Extraction method count:1
-    Metadata extraction method:Extract from file/folder names
-    Metadata source:File name
-    Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)
-    Regular expression to extract from folder name:(?P<field1>.*)
-    Extract metadata from:All images
-    Select the filtering criteria:and (file does contain "")
-    Metadata file location:
-    Match file and image metadata:[]
-    Use case insensitive matching?:No
-
-NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
-    Assign a name to:Images matching rules
-    Select the image type:Grayscale image
-    Name to assign these images:DNA
-    Match metadata:[]
-    Image set matching method:Order
-    Set intensity range from:Image metadata
-    Assignments count:1
-    Single images count:0
-    Maximum intensity:255.0
-    Process as 3D?:No
-    Relative pixel spacing in X:1.0
-    Relative pixel spacing in Y:1.0
-    Relative pixel spacing in Z:1.0
-    Select the rule criteria:and (file does startwith "im")
-    Name to assign these images:DNA
-    Name to assign these objects:Cell
-    Select the image type:Grayscale image
-    Set intensity range from:Image metadata
-    Select the image type:Grayscale image
-    Maximum intensity:255.0
-
-Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
-    Do you want to group your images?:Yes
-    grouping metadata count:1
-    Metadata category:Screen
-
-MeasureObjectSizeShape:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:1|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
-    Select objects to measure:Nuclei
-    Select objects to measure:Nucleoli
-    Calculate the Zernike features?:Yes
diff -r 3c3cd68d6d5a -r 27396311a314 test-data/measure_texture.cppipe
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/measure_texture.cppipe	Mon May 11 07:45:07 2020 -0400
@@ -0,0 +1,62 @@
+CellProfiler Pipeline: http://www.cellprofiler.org
+Version:3
+DateRevision:319
+GitHash:
+ModuleCount:5
+HasImagePlaneDetails:False
+
+Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    :
+    Filter images?:Images only
+    Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
+
+Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    Extract metadata?:Yes
+    Metadata data type:Text
+    Metadata types:{}
+    Extraction method count:1
+    Metadata extraction method:Extract from file/folder names
+    Metadata source:File name
+    Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)
+    Regular expression to extract from folder name:(?P<folderField1>.*)
+    Extract metadata from:All images
+    Select the filtering criteria:and (file does contain "")
+    Metadata file location:
+    Match file and image metadata:[]
+    Use case insensitive matching?:No
+
+NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Assign a name to:Images matching rules
+    Select the image type:Grayscale image
+    Name to assign these images:DNA
+    Match metadata:[]
+    Image set matching method:Order
+    Set intensity range from:Image metadata
+    Assignments count:1
+    Single images count:0
+    Maximum intensity:255.0
+    Process as 3D?:No
+    Relative pixel spacing in X:1.0
+    Relative pixel spacing in Y:1.0
+    Relative pixel spacing in Z:1.0
+    Select the rule criteria:and (file does startwith "im")
+    Name to assign these images:DNA
+    Name to assign these objects:Cell
+    Select the image type:Grayscale image
+    Set intensity range from:Image metadata
+    Select the image type:Grayscale image
+    Maximum intensity:255.0
+
+Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Do you want to group your images?:Yes
+    grouping metadata count:1
+    Metadata category:field1
+
+MeasureTexture:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:5|show_window:False|notes:\x5B\'PARAMS\x3A\', \'- Texture scale']|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Hidden:1
+    Hidden:1
+    Hidden:1
+    Select an image to measure:DNA
+    Select objects to measure:Nuclei
+    Texture scale to measure:3
+    Measure images or objects?:Objects
diff -r 3c3cd68d6d5a -r 27396311a314 test-data/measure_texture.txt
--- a/test-data/measure_texture.txt	Thu Apr 16 05:29:02 2020 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,62 +0,0 @@
-CellProfiler Pipeline: http://www.cellprofiler.org
-Version:3
-DateRevision:319
-GitHash:
-ModuleCount:5
-HasImagePlaneDetails:False
-
-Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
-    :
-    Filter images?:Images only
-    Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
-
-Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
-    Extract metadata?:Yes
-    Metadata data type:Text
-    Metadata types:{}
-    Extraction method count:1
-    Metadata extraction method:Extract from file/folder names
-    Metadata source:File name
-    Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)
-    Regular expression to extract from folder name:(?P<field1>.*)
-    Extract metadata from:All images
-    Select the filtering criteria:and (file does contain "")
-    Metadata file location:
-    Match file and image metadata:[]
-    Use case insensitive matching?:No
-
-NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
-    Assign a name to:Images matching rules
-    Select the image type:Grayscale image
-    Name to assign these images:DNA
-    Match metadata:[]
-    Image set matching method:Order
-    Set intensity range from:Image metadata
-    Assignments count:1
-    Single images count:0
-    Maximum intensity:255.0
-    Process as 3D?:No
-    Relative pixel spacing in X:1.0
-    Relative pixel spacing in Y:1.0
-    Relative pixel spacing in Z:1.0
-    Select the rule criteria:and (file does startwith "im")
-    Name to assign these images:DNA
-    Name to assign these objects:Cell
-    Select the image type:Grayscale image
-    Set intensity range from:Image metadata
-    Select the image type:Grayscale image
-    Maximum intensity:255.0
-
-Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
-    Do you want to group your images?:Yes
-    grouping metadata count:1
-    Metadata category:Screen
-
-MeasureTexture:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:5|show_window:False|notes:\x5B\'PARAMS\x3A\', \'- Texture scale']|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
-    Hidden:1
-    Hidden:1
-    Hidden:1
-    Select an image to measure:DNA
-    Select objects to measure:Nuclei
-    Texture scale to measure:3
-    Measure images or objects?:Objects
diff -r 3c3cd68d6d5a -r 27396311a314 test-data/relate_objects.cppipe
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/relate_objects.cppipe	Mon May 11 07:45:07 2020 -0400
@@ -0,0 +1,62 @@
+CellProfiler Pipeline: http://www.cellprofiler.org
+Version:3
+DateRevision:319
+GitHash:
+ModuleCount:5
+HasImagePlaneDetails:False
+
+Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    :
+    Filter images?:Images only
+    Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
+
+Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    Extract metadata?:Yes
+    Metadata data type:Text
+    Metadata types:{}
+    Extraction method count:1
+    Metadata extraction method:Extract from file/folder names
+    Metadata source:File name
+    Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)
+    Regular expression to extract from folder name:(?P<folderField1>.*)
+    Extract metadata from:All images
+    Select the filtering criteria:and (file does contain "")
+    Metadata file location:
+    Match file and image metadata:[]
+    Use case insensitive matching?:No
+
+NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Assign a name to:Images matching rules
+    Select the image type:Grayscale image
+    Name to assign these images:DNA
+    Match metadata:[]
+    Image set matching method:Order
+    Set intensity range from:Image metadata
+    Assignments count:1
+    Single images count:0
+    Maximum intensity:255.0
+    Process as 3D?:No
+    Relative pixel spacing in X:1.0
+    Relative pixel spacing in Y:1.0
+    Relative pixel spacing in Z:1.0
+    Select the rule criteria:and (file does startwith "im")
+    Name to assign these images:DNA
+    Name to assign these objects:Cell
+    Select the image type:Grayscale image
+    Set intensity range from:Image metadata
+    Select the image type:Grayscale image
+    Maximum intensity:255.0
+
+Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Do you want to group your images?:Yes
+    grouping metadata count:1
+    Metadata category:field1
+
+RelateObjects:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:5|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Parent objects:Nuclei
+    Child objects:Nucleoli
+    Calculate child-parent distances?:Both
+    Calculate per-parent means for all child measurements?:Yes
+    Calculate distances to other parents?:No
+    Do you want to save the children with parents as a new object set?:Yes
+    Name the output object:RelateObjects
diff -r 3c3cd68d6d5a -r 27396311a314 test-data/relate_objects.txt
--- a/test-data/relate_objects.txt	Thu Apr 16 05:29:02 2020 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,62 +0,0 @@
-CellProfiler Pipeline: http://www.cellprofiler.org
-Version:3
-DateRevision:319
-GitHash:
-ModuleCount:5
-HasImagePlaneDetails:False
-
-Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
-    :
-    Filter images?:Images only
-    Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
-
-Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
-    Extract metadata?:Yes
-    Metadata data type:Text
-    Metadata types:{}
-    Extraction method count:1
-    Metadata extraction method:Extract from file/folder names
-    Metadata source:File name
-    Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)
-    Regular expression to extract from folder name:(?P<field1>.*)
-    Extract metadata from:All images
-    Select the filtering criteria:and (file does contain "")
-    Metadata file location:
-    Match file and image metadata:[]
-    Use case insensitive matching?:No
-
-NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
-    Assign a name to:Images matching rules
-    Select the image type:Grayscale image
-    Name to assign these images:DNA
-    Match metadata:[]
-    Image set matching method:Order
-    Set intensity range from:Image metadata
-    Assignments count:1
-    Single images count:0
-    Maximum intensity:255.0
-    Process as 3D?:No
-    Relative pixel spacing in X:1.0
-    Relative pixel spacing in Y:1.0
-    Relative pixel spacing in Z:1.0
-    Select the rule criteria:and (file does startwith "im")
-    Name to assign these images:DNA
-    Name to assign these objects:Cell
-    Select the image type:Grayscale image
-    Set intensity range from:Image metadata
-    Select the image type:Grayscale image
-    Maximum intensity:255.0
-
-Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
-    Do you want to group your images?:Yes
-    grouping metadata count:1
-    Metadata category:Screen
-
-RelateObjects:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:5|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
-    Parent objects:Nuclei
-    Child objects:Nucleoli
-    Calculate child-parent distances?:Both
-    Calculate per-parent means for all child measurements?:Yes
-    Calculate distances to other parents?:No
-    Do you want to save the children with parents as a new object set?:Yes
-    Name the output object:RelateObjects
diff -r 3c3cd68d6d5a -r 27396311a314 test-data/save_images.cppipe
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/save_images.cppipe	Mon May 11 07:45:07 2020 -0400
@@ -0,0 +1,71 @@
+CellProfiler Pipeline: http://www.cellprofiler.org
+Version:3
+DateRevision:319
+GitHash:
+ModuleCount:5
+HasImagePlaneDetails:False
+
+Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    :
+    Filter images?:Images only
+    Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
+
+Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    Extract metadata?:Yes
+    Metadata data type:Text
+    Metadata types:{}
+    Extraction method count:1
+    Metadata extraction method:Extract from file/folder names
+    Metadata source:File name
+    Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)
+    Regular expression to extract from folder name:(?P<folderField1>.*)
+    Extract metadata from:All images
+    Select the filtering criteria:and (file does contain "")
+    Metadata file location:
+    Match file and image metadata:[]
+    Use case insensitive matching?:No
+
+NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Assign a name to:Images matching rules
+    Select the image type:Grayscale image
+    Name to assign these images:DNA
+    Match metadata:[]
+    Image set matching method:Order
+    Set intensity range from:Image metadata
+    Assignments count:1
+    Single images count:0
+    Maximum intensity:255.0
+    Process as 3D?:No
+    Relative pixel spacing in X:1.0
+    Relative pixel spacing in Y:1.0
+    Relative pixel spacing in Z:1.0
+    Select the rule criteria:and (file does startwith "im")
+    Name to assign these images:DNA
+    Name to assign these objects:Cell
+    Select the image type:Grayscale image
+    Set intensity range from:Image metadata
+    Select the image type:Grayscale image
+    Maximum intensity:255.0
+
+Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Do you want to group your images?:Yes
+    grouping metadata count:1
+    Metadata category:field1
+
+SaveImages:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:13|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Select the type of image to save:Image
+    Select the image to save:ImageDisplay
+    Select method for constructing file names:From image filename
+    Select image name for file prefix:DNA
+    Enter single file name:OrigBlue
+    Number of digits:4
+    Append a suffix to the image file name?:Yes
+    Text to append to the image name:_nucleiNumbers
+    Saved file format:tiff
+    Output file location:Default Output Folder\x7Coutput
+    Image bit depth:8-bit integer
+    Overwrite existing files without warning?:Yes
+    When to save:Every cycle
+    Record the file and path information to the saved image?:No
+    Create subfolders in the output folder?:No
+    Base image folder:Elsewhere...
diff -r 3c3cd68d6d5a -r 27396311a314 test-data/save_images.txt
--- a/test-data/save_images.txt	Thu Apr 16 05:29:02 2020 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,71 +0,0 @@
-CellProfiler Pipeline: http://www.cellprofiler.org
-Version:3
-DateRevision:319
-GitHash:
-ModuleCount:5
-HasImagePlaneDetails:False
-
-Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
-    :
-    Filter images?:Images only
-    Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
-
-Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
-    Extract metadata?:Yes
-    Metadata data type:Text
-    Metadata types:{}
-    Extraction method count:1
-    Metadata extraction method:Extract from file/folder names
-    Metadata source:File name
-    Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)
-    Regular expression to extract from folder name:(?P<field1>.*)
-    Extract metadata from:All images
-    Select the filtering criteria:and (file does contain "")
-    Metadata file location:
-    Match file and image metadata:[]
-    Use case insensitive matching?:No
-
-NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
-    Assign a name to:Images matching rules
-    Select the image type:Grayscale image
-    Name to assign these images:DNA
-    Match metadata:[]
-    Image set matching method:Order
-    Set intensity range from:Image metadata
-    Assignments count:1
-    Single images count:0
-    Maximum intensity:255.0
-    Process as 3D?:No
-    Relative pixel spacing in X:1.0
-    Relative pixel spacing in Y:1.0
-    Relative pixel spacing in Z:1.0
-    Select the rule criteria:and (file does startwith "im")
-    Name to assign these images:DNA
-    Name to assign these objects:Cell
-    Select the image type:Grayscale image
-    Set intensity range from:Image metadata
-    Select the image type:Grayscale image
-    Maximum intensity:255.0
-
-Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
-    Do you want to group your images?:Yes
-    grouping metadata count:1
-    Metadata category:Screen
-
-SaveImages:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:13|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
-    Select the type of image to save:Image
-    Select the image to save:ImageDisplay
-    Select method for constructing file names:From image filename
-    Select image name for file prefix:DNA
-    Enter single file name:OrigBlue
-    Number of digits:4
-    Append a suffix to the image file name?:Yes
-    Text to append to the image name:_nucleiNumbers
-    Saved file format:tiff
-    Output file location:Default Output Folder\x7Coutput
-    Image bit depth:8-bit integer
-    Overwrite existing files without warning?:Yes
-    When to save:Every cycle
-    Record the file and path information to the saved image?:No
-    Create subfolders in the output folder?:No
-    Base image folder:Elsewhere...