Mercurial > repos > lldelisle > omero_hyperstack_to_gastruloid_measurements
diff omero_hyperstack_to_gastruloid_measurements.xml @ 2:45375dc5dd8d draft default tip
planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_gastruloid_measurements commit 5e181f51312e53a72d354584439fa9359cd16723-dirty
| author | lldelisle |
|---|---|
| date | Thu, 15 Feb 2024 12:28:09 +0000 |
| parents | bd5771ff6aa3 |
| children |
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--- a/omero_hyperstack_to_gastruloid_measurements.xml Wed Dec 20 20:07:13 2023 +0000 +++ b/omero_hyperstack_to_gastruloid_measurements.xml Thu Feb 15 12:28:09 2024 +0000 @@ -1,6 +1,6 @@ <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@">20231220</token> + <token name="@TOOL_VERSION@">20240214</token> <xml name="segmentation"> <conditional name="use_ilastik"> <param name="segmentation_method" type="select" label="Segmentation method"> @@ -29,8 +29,28 @@ <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" /> @@ -40,18 +60,34 @@ </section> </when> </conditional> - <param name="radius_median" type="float" value="20" label="Radius for median (=smooth the mask)" /> - <param name="min_size_particle" type="integer" min="0" value="5000" label="Minimum surface for Analyze Particle" /> + <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="20220414">fiji</requirement> + <requirement type="package" version="20231211">fiji</requirement> <requirement type="package" version="3.7">python</requirement> - <requirement type="package" version="2.0.0">fiji-max_inscribed_circles</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="5.8.0">fiji-omero_ij</requirement> - <requirement type="package" version="5.12.2">fiji-simple_omero_client</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 @@ -75,7 +111,7 @@ ## 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="${minimum_diameter}",closeness_tolerance="${closeness_tolerance}",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}"' > output.log + '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> @@ -113,17 +149,26 @@ </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="spine_only">Recompute only spine</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> @@ -138,15 +183,16 @@ <param name="probability_threshold_BG" type="hidden" value="0"/> </section> </section> - <param name="radius_median" type="hidden" value="20" /> - <param name="min_size_particle" type="hidden" value="5000" /> + <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" type="integer" min="0" value="20" label="Minimum diameter of inscribed circles" /> - <param name="closeness_tolerance" type="integer" min="0" value="50" label="Closeness Tolerance for the spine" help="Maximum distance between circles along the spine"/> + <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)" /> @@ -188,7 +234,7 @@ /* * = COPYRIGHT = - * © All rights reserved. ECOLE POLYTECHNIQUE FEDERALE DE LAUSANNE, Switzerland, BioImaging And Optics Platform (BIOP), 2023 + * © 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