annotate imagej2_adjust_threshold_binary.xml @ 2:da29019170f1 draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
author imgteam
date Sun, 05 Nov 2023 10:52:33 +0000
parents 29a4d422f32a
children 2b007b1e6c1b
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2
da29019170f1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
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1 <tool id="imagej2_adjust_threshold_binary" name="Adjust threshold" version="@WRAPPER_VERSION@.1">
da29019170f1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
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2 <description>with ImageJ2</description>
0
f1ba33cd9edf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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3 <macros>
f1ba33cd9edf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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4 <import>imagej2_macros.xml</import>
f1ba33cd9edf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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5 </macros>
2
da29019170f1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
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6 <edam_operations>
da29019170f1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
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7 <edam_operation>operation_3443</edam_operation>
da29019170f1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
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8 </edam_operations>
da29019170f1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
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9 <xrefs>
da29019170f1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
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10 <xref type="bio.tools">imagej</xref>
da29019170f1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
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11 <xref type="biii">imagej2</xref>
da29019170f1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
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12 </xrefs>
1
29a4d422f32a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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13 <expand macro="fiji_requirements"/>
29a4d422f32a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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14 <command detect_errors="exit_code"><![CDATA[
29a4d422f32a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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15 #import os
29a4d422f32a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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16 #set error_log = 'output_log.txt'
29a4d422f32a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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17 #set input_sans_ext = $os.path.splitext($os.path.basename($input.file_name))[0]
29a4d422f32a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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18 #set input_with_ext = '.'.join([input_sans_ext, $input.ext])
29a4d422f32a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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19 ln -s '$input.file_name' '$input_with_ext' &&
29a4d422f32a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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20 #set output_filename = '.'.join(['output', $input.ext])
29a4d422f32a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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21 touch '$output_filename' &&
29a4d422f32a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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22 touch '$error_log' &&
29a4d422f32a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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23 ImageJ --ij2 --headless --debug
29a4d422f32a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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24 --jython '$__tool_directory__/imagej2_adjust_threshold_binary_jython_script.py'
29a4d422f32a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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25 '$error_log'
29a4d422f32a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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26 '$input_with_ext'
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27 $threshold_min
29a4d422f32a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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28 $threshold_max
29a4d422f32a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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29 '$method'
29a4d422f32a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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30 '$display'
29a4d422f32a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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31 '$black_background'
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32 '$stack_histogram'
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33 '$output_filename'
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34 '$input.ext'
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35 &>'$error_log';
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36 if [[ $? -ne 0 ]]; then
29a4d422f32a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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37 cat '$error_log' >&2;
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38 else
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39 mv '$output_filename' '$output';
29a4d422f32a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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40 fi
29a4d422f32a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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41 ]]></command>
0
f1ba33cd9edf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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42 <inputs>
1
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43 <expand macro="param_input"/>
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44 <param name="threshold_min" type="float" value="0" min="0" max="255" label="Minimum threshold value"/>
29a4d422f32a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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45 <param name="threshold_max" type="float" value="0" min="0" max="255" label="Maximum threshold value"/>
0
f1ba33cd9edf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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46 <param name="method" type="select" label="Method" help="The Default method is the modified IsoData algorithm.">
f1ba33cd9edf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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47 <option value="Default" selected="True">Default</option>
f1ba33cd9edf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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48 <option value="Huang">Huang</option>
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49 <option value="Intermodes">Intermodes</option>
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50 <option value="IsoData">IsoData</option>
f1ba33cd9edf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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51 <option value="IJ_IsoData">IJ_IsoData</option>
f1ba33cd9edf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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52 <option value="Li">Li</option>
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53 <option value="MaxEntropy">MaxEntropy</option>
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54 <option value="Mean">Mean</option>
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55 <option value="MinError">MinError</option>
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56 <option value="Minimum">Minimum</option>
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57 <option value="Moments">Moments</option>
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58 <option value="Otsu">Otsu</option>
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59 <option value="RenyiEntropy">RenyiEntropy</option>
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60 <option value="Shanbhag">Shanbhag</option>
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61 <option value="Triangle">Triangle</option>
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62 <option value="Yen">Yen</option>
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63 </param>
f1ba33cd9edf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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64 <param name="display" type="select" label="Display">
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65 <option value="red" selected="True">Red</option>
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66 <option value="bw">Black and White</option>
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67 <option value="over_under">Over/Under</option>
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68 </param>
f1ba33cd9edf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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69 <param name="black_background" type="select" label="Black background" help="Select yes if features are lighter than the background.">
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70 <option value="no" selected="True">No</option>
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71 <option value="yes">Yes</option>
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72 </param>
f1ba33cd9edf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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73 <param name="stack_histogram" type="select" label="Stack histogram" help="Select yes to first compute the histogram of the whole stack (or hyperstack) and then compute the threshold based on that histogram.">
f1ba33cd9edf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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74 <option value="no" selected="True">No</option>
f1ba33cd9edf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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75 <option value="yes">Yes</option>
f1ba33cd9edf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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76 </param>
f1ba33cd9edf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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77 </inputs>
f1ba33cd9edf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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78 <outputs>
1
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79 <data name="output" format_source="input"/>
0
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80 </outputs>
f1ba33cd9edf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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81 <tests>
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82 <test>
1
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83 <param name="input" value="blobs.gif"/>
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84 <param name="output_datatype" value="gif"/>
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85 <param name="threshold_min" value="0.0"/>
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86 <param name="threshold_max" value="129.0"/>
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87 <param name="method" value="Default"/>
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88 <param name="display" value="red"/>
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89 <param name="black_background" value="no"/>
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90 <param name="stack_histogram" value="no"/>
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91 <output name="output" file="blobs_threshold_default.gif" compare="sim_size"/>
0
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92 </test>
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93 <test>
1
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94 <param name="input" value="blobs.gif"/>
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95 <param name="output_datatype" value="gif"/>
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96 <param name="threshold_min" value="118.0"/>
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97 <param name="threshold_max" value="255.0"/>
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98 <param name="method" value="IJ_IsoData"/>
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99 <param name="display" value="over_under"/>
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100 <param name="black_background" value="no"/>
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101 <param name="stack_histogram" value="no"/>
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102 <output name="output" file="blobs_threshold_ijiso.gif" compare="sim_size"/>
0
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103 </test>
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104 <test>
1
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105 <param name="input" value="blobs.gif"/>
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106 <param name="output_datatype" value="gif"/>
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107 <param name="threshold_min" value="72.0"/>
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108 <param name="threshold_max" value="255.0"/>
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109 <param name="method" value="Huang"/>
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110 <param name="display" value="bw"/>
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111 <param name="black_background" value="yes"/>
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112 <param name="stack_histogram" value="no"/>
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113 <output name="output" file="blobs_threshold_huang_dark.gif" compare="sim_size"/>
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114 </test>
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115 </tests>
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116 <help>
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117
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118 @requires_binary_input@
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119
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120 **What it does**
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121
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122 <![CDATA[
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123 Sets lower and upper threshold values, segmenting grayscale images into features of interest and background
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124
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125 - **Minimum threshold value** - Adjusts the minimum threshold value.
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126 - **Maximum threshold value** - Adjusts the maximum threshold value.
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127 - **Method** - Allows any of the 16 different automatic thresholding methods to be selected. These are global thresholding methods that typically cannot deal with unevenly illuminated images (such as in brightfield microscopy)."
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128 - **Display** - Selects one of three display mode: **Red** displays the thresholded values in red, **Black and White** features are displayed in black and background in white, **Over/Under** displays pixels below the lower threshold value in blue, thresholded pixels in grayscale, and pixels above the upper threshold value in green.
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129 - **Black background** - Select **yes** when features are lighter than the background.
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130 - **Stack histogram**  Select **yes** to first compute the histogram of the whole stack (or hyperstack) and then compute the threshold based on that histogram. As such, all slices are binarized using the single computed value. If unchecked, the threshold of each slice is computed separately.
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131 ]]>
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132
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133 </help>
1
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134 <expand macro="fiji_headless_citations"/>
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135 </tool>