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| author | lldelisle |
|---|---|
| date | Thu, 15 Feb 2024 12:28:09 +0000 |
| parents | bd5771ff6aa3 |
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<tool id="omero_hyperstack_to_gastruloid_measurements" name="Omero hyperstack to Gastruloid measurements" profile="20.01" version="@TOOL_VERSION@+galaxy0"> <macros> <token name="@TOOL_VERSION@">20240214</token> <xml name="segmentation"> <conditional name="use_ilastik"> <param name="segmentation_method" type="select" label="Segmentation method"> <option value="convert_to_mask">Simply convert to mask</option> <option value="ilastik">Use an ilastik project</option> </param> <when value="ilastik"> <param name="ilastik_project" type="data" format="h5" label="Ilastik project" /> <param name="ilastik_project_type" type="select" label="Type of Ilastik project"> <option value="Regular">Regular</option> <option value="Auto-context">Auto-context</option> </param> <param name="ilastik_label_OI" type="integer" value="3" label="Index of label of interest in Ilastik project" /> <param name="probability_threshold" type="float" min="0" max="1" value="0.4" label="Probability threshold for ilastik" /> <conditional name="background"> <param name="get_background" type="select" label="Get ROI with background" help="Can be useful to normalize fluo"> <option value="yes">Yes</option> <option value="no">No</option> </param> <when value="yes"> <param name="ilastik_label_BG" type="integer" value="1" label="Index of label of background in Ilastik project" /> <param name="probability_threshold_BG" type="float" min="0" max="1" value="0.8" label="Probability threshold for background in ilastik" /> </when> <when value="no"> <param name="ilastik_label_BG" type="hidden" value="0"/> <param name="probability_threshold_BG" type="hidden" value="0"/> </when> </conditional> <param name="thresholding_method" type="hidden" value="Default"/> </when> <when value="convert_to_mask"> <param name="thresholding_method" type="select" label="Thresholding method" help="Method to use in the convert to mask"> <option value="Default">Default</option> <option value="Huang">Huang</option> <option value="Intermodes">Intermodes</option> <option value="IsoData">IsoData</option> <option value="IJ_IsoData">IJ_IsoData</option> <option value="Li">Li</option> <option value="MaxEntropy">MaxEntropy</option> <option value="Mean">Mean</option> <option value="MinError">MinError</option> <option value="Minimum">Minimum</option> <option value="Moments">Moments</option> <option value="Otsu">Otsu</option> <option value="Percentile">Percentile</option> <option value="RenyiEntropy">RenyiEntropy</option> <option value="Shanbhag">Shanbhag</option> <option value="Triangle">Triangle</option> <option value="Yen">Yen</option> </param> <param name="ilastik_project_type" type="hidden" value="Regular" /> <param name="ilastik_label_OI" type="hidden" value="3" /> <param name="probability_threshold" type="hidden" value="0" /> <section name="background" title="" > <param name="ilastik_label_BG" type="hidden" value="0"/> <param name="probability_threshold_BG" type="hidden" value="0"/> </section> </when> </conditional> <section name="options" title="Options..." expanded="false" > <param name="options_do" type="select" label="In Options... do=" help="Operation to perform after thresholding"> <option value="Nothing">Nothing</option> <option value="Erode">Erode</option> <option value="Dilate">Dilate</option> <option value="Open">Open</option> <option value="Close">Close</option> <option value="Outline">Outline</option> <option value="Fill">Fill</option> <option value="Holes">Holes</option> <option value="Skeletonize">Skeletonize</option> </param> <param name="options_iteration" type="integer" min="1" value="1" label="In Options... iteration=" /> <param name="options_count" type="integer" min="1" max="8" value="1" label="In Options... count=" /> </section> <param name="fill_holes_before_median" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Fill holes before the Median..." /> <param name="radius_median" type="float" value="10" label="Radius for median (=smooth the mask)" /> <param name="min_size_particle" type="float" min="0" value="20000" label="Minimum surface for Analyze Particle" /> <param name="keep_only_largest" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Keep only one gastruloid per timepoint" /> </xml> </macros> <requirements> <requirement type="package" version="20231211">fiji</requirement> <requirement type="package" version="3.7">python</requirement> <requirement type="package" version="2.1.0">fiji-max_inscribed_circles</requirement> <requirement type="package" version="1.8.2">fiji-ilastik</requirement> <requirement type="package" version="5.8.3">fiji-omero_ij</requirement> <requirement type="package" version="5.16.0">fiji-simple_omero_client</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ ## the user wants to use a non-public OMERO instance ## check if credentials are set in the user-preferences, if not warn the user and exit #set $username = $__user__.extra_preferences.get('omero_account|username', "") #set $password = $__user__.extra_preferences.get('omero_account|password', "") #if ($username == "" or $password ==""): echo "OMERO connection credentials are empty. Set your credentials via: User -> Preferences -> Manage Information" 1>&2 && exit 1 && #end if #if str($mode.use_ilastik.segmentation_method) == "ilastik": #set $ilastik_project_file = str($mode.use_ilastik.ilastik_project) #set $ilastik_project_name = str($mode.use_ilastik.ilastik_project.name) #else #set $ilastik_project_file = "inexisting.ilp" #set $ilastik_project_name = "inexisting.ilp" #end if mkdir output && ## Because ilastik wants to write to ${HOME}/.cache and ${HOME}/.config export HOME=`pwd` && ImageJ-ilastik --ij2 --headless --console --run '$__tool_directory__/'1-omero_timelapse_image_to_measurements_phase.groovy 'USERNAME="",PASSWORD="",credentials="${credentials}",host="${omero_host}",port="${omero_port}",object_type="${omero_object.object_type}",id="${omero_object.omero_id}",segmentation_method="${mode.use_ilastik.segmentation_method}",use_existing="${mode.use_existing}",ilastik_project="$ilastik_project_file",ilastik_project_short_name="$ilastik_project_name",ilastik_project_type="${mode.use_ilastik.ilastik_project_type}",ilastik_label_OI="${mode.use_ilastik.ilastik_label_OI}",probability_threshold="${mode.use_ilastik.probability_threshold}",radius_median="${mode.radius_median}",min_size_particle="${mode.min_size_particle}",get_spine="true",minimum_diameter_um="${minimum_diameter_um}",closeness_tolerance_um="${closeness_tolerance_um}",min_similarity="${min_similarity}",output_directory="output",debug="${debug}",rescue="${mode.rescue}",ilastik_label_BG="${mode.use_ilastik.background.ilastik_label_BG}",probability_threshold_BG="${mode.use_ilastik.background.probability_threshold_BG}",keep_only_largest="${mode.keep_only_largest}",replace_at_runtime="${mode.replace_at_runtime}",thresholding_method="${mode.use_ilastik.thresholding_method}",options_do="${mode.options.options_do}",options_iteration="${mode.options.options_iteration}",options_count="${mode.options.options_count}",fill_holes_before_median="${mode.fill_holes_before_median}"' > output.log ]]> </command> <configfiles> <configfile name="credentials"><![CDATA[#set $username = $__user__.extra_preferences.get('omero_account|username', "") #set $password = $__user__.extra_preferences.get('omero_account|password', "") $username $password ]]></configfile> </configfiles> <inputs> <param name="omero_host" type="text" label="OMERO host URL"> <validator type="regex" message="Enter a valid host location, for example, your.omero.server">^[a-zA-Z0-9._-]*$</validator> <validator type="expression" message="No two dots (..) allowed">'..' not in value</validator> </param> <param name="omero_port" type="integer" value="4064" label="Omero port" /> <conditional name="omero_object"> <param name="object_type" type="select" label="Type of object to analyze"> <option value="image">Single Omero Image</option> <option value="well">All images of a Well</option> <option value="plate">All images of a Plate</option> <option value="dataset">All images of a Dataset</option> </param> <when value="image"> <param name="omero_id" type="integer" value="" label="Image ID on omero" /> </when> <when value="well"> <param name="omero_id" type="integer" value="" label="Well ID on omero" /> </when> <when value="plate"> <param name="omero_id" type="integer" value="" label="Plate ID on omero" /> </when> <when value="dataset"> <param name="omero_id" type="integer" value="" label="Dataset ID on omero" /> </when> </conditional> <conditional name="mode"> <param name="mode_select" type="select" label="Which mode do you want to use?" > <option value="replace_existing">Replace existing (not recommanded with Ilastik)</option> <option value="spine_only">Recompute only spine</option> <option value="regular">Regular (from scratch)</option> <option value="rescue">Rescue (if Regular did not go to the end)</option> </param> <when value="replace_existing"> <expand macro="segmentation"/> <param name="replace_at_runtime" type="hidden" value="true"/> <param name="rescue" type="hidden" value="false"/> <param name="use_existing" type="hidden" value="false"/> </when> <when value="regular"> <expand macro="segmentation"/> <param name="replace_at_runtime" type="hidden" value="false"/> <param name="rescue" type="hidden" value="false"/> <param name="use_existing" type="hidden" value="false"/> </when> <when value="rescue"> <expand macro="segmentation"/> <param name="replace_at_runtime" type="hidden" value="false"/> <param name="rescue" type="hidden" value="true"/> <param name="use_existing" type="hidden" value="false"/> </when> <when value="spine_only"> <section name="use_ilastik" title="" > <param name="segmentation_method" type="hidden" value="convert_to_mask" /> <param name="ilastik_project_type" type="hidden" value="Regular" /> <param name="ilastik_label_OI" type="hidden" value="3" /> <param name="probability_threshold" type="hidden" value="0" /> <section name="background" title="" > <param name="ilastik_label_BG" type="hidden" value="0"/> <param name="probability_threshold_BG" type="hidden" value="0"/> </section> </section> <param name="replace_at_runtime" type="hidden" value="false"/> <param name="radius_median" type="hidden" value="10" /> <param name="min_size_particle" type="hidden" value="20000" /> <param name="keep_only_largest" type="hidden" value="true"/> <param name="rescue" type="hidden" value="false"/> <param name="use_existing" type="hidden" value="true"/> </when> </conditional> <param name="minimum_diameter_um" type="float" min="0" value="40" label="Minimum diameter of inscribed circles (in um)" /> <param name="closeness_tolerance_um" type="float" min="0" value="50" label="Closeness Tolerance for the spine (in um)" help="Maximum distance between circles along the spine"/> <param name="min_similarity" type="float" min="-1" max="1" value="0.1" label="Min similarity for the spine" help="Close to 0 values allow more U shapes while close to 1 values only allows I shapes" /> <param name="debug" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Debug the elongation index" help="This will output all inscribed circles" /> <param name="keep_intermediate" type="boolean" checked="false" label="Keep intermediate results (ilastik prediction + tables)" /> </inputs> <outputs> <data name="logfile" format="txt" from_work_dir="output.log" label="${tool.name} on ${omero_object.object_type} ID ${omero_object.omero_id} with $getVar('mode.use_ilastik.ilastik_project.name', 'no ilastik'): logfile"> </data> <collection name="tables" type="list" label="${tool.name} on ${omero_object.object_type} ID ${omero_object.omero_id} with $getVar('mode.use_ilastik.ilastik_project.name', 'no ilastik'): Tables"> <discover_datasets pattern="(?P<designation>.+)\.csv" directory="output" format="csv"/> <filter>keep_intermediate</filter> </collection> <collection name="hyperstacks_with_overlay" type="list" label="${tool.name} on ${omero_object.object_type} ID ${omero_object.omero_id} with $getVar('mode.use_ilastik.ilastik_project.name', 'no ilastik'): Hyperstacks"> <discover_datasets pattern="(?P<designation>.+)\.tiff" directory="output" format="tiff"/> </collection> <collection name="ilastik_results" type="list" label="${tool.name} on ${omero_object.object_type} ID ${omero_object.omero_id} with $getVar('mode.use_ilastik.ilastik_project.name', 'no ilastik'): Ilastik"> <discover_datasets pattern="(?P<designation>.+)\.tif$" directory="output" format="tiff"/> <filter>keep_intermediate and mode['use_ilastik']['segmentation_method'] == "ilastik"</filter> </collection> </outputs> <help> <![CDATA[ **Overview** This tool will get images from omero, use an ilastik project to get propability and generate a mask. The potential gastruloids will be indentified by analyze Particles. On each ROI, the elongation index will be computed. **License** License text:: // This macro was written by the BIOP (https://github.com/BIOP) // Romain Guiet and Rémy Dornier // Lucille Delisle modified to support headless // And to be more robust to OMERO reboot // merge the analysis script with templates available at // https://github.com/BIOP/OMERO-scripts/tree/025047955b5c1265e1a93b259c1de4600d00f107/Fiji /* * = COPYRIGHT = * © All rights reserved. ECOLE POLYTECHNIQUE FEDERALE DE LAUSANNE, Switzerland, BioImaging And Optics Platform (BIOP), 2024 * * Licensed under the BSD-3-Clause License: * Redistribution and use in source and binary forms, with or without modification, are permitted provided * that the following conditions are met: * 1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * 2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer * in the documentation and/or other materials provided with the distribution. * 3. Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products * derived from this software without specific prior written permission. * * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, * BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. * IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, * EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, * STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. */ ]]> </help> </tool>