From 3a2a1522226fd5e485de37b6107ef50a976e476e Mon Sep 17 00:00:00 2001 From: Lucille Delisle Date: Wed, 20 Dec 2023 18:15:07 +0100 Subject: [PATCH 1/2] update omero_hyperstack_to_gastruloid_measurement + add README with CHANGELOG --- .tt_skip | 2 - .../.shed.yml | 2 +- ...melapse_image_to_measurements_phase.groovy | 207 ++++++++++-------- .../README.md | 35 +++ ..._hyperstack_to_gastruloid_measurements.xml | 90 +++++--- 5 files changed, 203 insertions(+), 133 deletions(-) create mode 100644 tools/omero_hyperstack_to_gastruloid_measurements/README.md diff --git a/.tt_skip b/.tt_skip index 494821b..3940fc6 100644 --- a/.tt_skip +++ b/.tt_skip @@ -1,6 +1,4 @@ tools/measure_gastruloids -tools/incucyte_stack_and_upload_omero/ tools/hyperstack_to_bleach_corrected_movie tools/omero_hyperstack_to_fluo_measurements_on_gastruloid -tools/omero_hyperstack_to_gastruloid_measurements tools/omero_clean_rois_tables diff --git a/tools/omero_hyperstack_to_gastruloid_measurements/.shed.yml b/tools/omero_hyperstack_to_gastruloid_measurements/.shed.yml index c40609a..8f2f113 100644 --- a/tools/omero_hyperstack_to_gastruloid_measurements/.shed.yml +++ b/tools/omero_hyperstack_to_gastruloid_measurements/.shed.yml @@ -3,5 +3,5 @@ categories: description: Analyse Hyperstack on OMERO server to segment gastruloid and compute measurements name: omero_hyperstack_to_gastruloid_measurements owner: lldelisle -long_description: Uses a groovy to 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. +long_description: Uses a groovy to get images from OMERO, use an ilastik project to get propability and generate a mask or simply autothreshold to mask. The potential gastruloids will be indentified by analyze Particles. On each ROI, the elongation index will be computed. remote_repository_url: https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_gastruloid_measurements diff --git a/tools/omero_hyperstack_to_gastruloid_measurements/1-omero_timelapse_image_to_measurements_phase.groovy b/tools/omero_hyperstack_to_gastruloid_measurements/1-omero_timelapse_image_to_measurements_phase.groovy index a11a9bb..d0c5078 100644 --- a/tools/omero_hyperstack_to_gastruloid_measurements/1-omero_timelapse_image_to_measurements_phase.groovy +++ b/tools/omero_hyperstack_to_gastruloid_measurements/1-omero_timelapse_image_to_measurements_phase.groovy @@ -5,7 +5,7 @@ // merge the analysis script with templates available at // https://github.com/BIOP/OMERO-scripts/tree/main/Fiji -// Last modification: 2023-07-28 +// Last modification: 2023-12-20 /* * = COPYRIGHT = @@ -29,7 +29,8 @@ * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. */ -// This macro will use ilastik to detect ROIs +// This macro will use ilastik or convert to mask +// to detect ROIs // measure and compute elongation index // It may also regenerate a ROI of background @@ -88,6 +89,7 @@ import ij.plugin.Duplicator import ij.plugin.frame.RoiManager import ij.plugin.HyperStackConverter import ij.plugin.ImageCalculator +import ij.plugin.Thresholder import ij.Prefs import ij.process.FloatPolygon import ij.process.ImageProcessor @@ -402,7 +404,7 @@ def processDataset(Client user_client, DatasetWrapper dataset_wrp, Boolean headless_mode, Boolean debug, String tool_version, Boolean use_existing, String final_object, Boolean rescue, Integer ilastik_label_BG, Double probability_threshold_BG, - Boolean keep_only_largest) { + Boolean keep_only_largest, String segmentation_method) { robustlyGetAll(dataset_wrp, "image", user_client).each{ ImageWrapper img_wrp -> processImage(user_client, img_wrp, ilastik_project, ilastik_project_type, @@ -414,7 +416,7 @@ def processDataset(Client user_client, DatasetWrapper dataset_wrp, headless_mode, debug, tool_version, use_existing, final_object, rescue, ilastik_label_BG, probability_threshold_BG, - keep_only_largest) + keep_only_largest, segmentation_method) } } @@ -429,7 +431,7 @@ def processSinglePlate(Client user_client, PlateWrapper plate_wrp, Boolean headless_mode, Boolean debug, String tool_version, Boolean use_existing, String final_object, Boolean rescue, Integer ilastik_label_BG, Double probability_threshold_BG, - Boolean keep_only_largest) { + Boolean keep_only_largest, String segmentation_method) { robustlyGetAll(plate_wrp, "well", user_client).each{ well_wrp -> processSingleWell(user_client, well_wrp, ilastik_project, ilastik_project_type, @@ -441,7 +443,7 @@ def processSinglePlate(Client user_client, PlateWrapper plate_wrp, headless_mode, debug, tool_version, use_existing, final_object, rescue, ilastik_label_BG, probability_threshold_BG, - keep_only_largest) + keep_only_largest, segmentation_method) } } @@ -456,7 +458,7 @@ def processSingleWell(Client user_client, WellWrapper well_wrp, Boolean headless_mode, Boolean debug, String tool_version, Boolean use_existing, String final_object, Boolean rescue, Integer ilastik_label_BG, Double probability_threshold_BG, - Boolean keep_only_largest) { + Boolean keep_only_largest, String segmentation_method) { well_wrp.getWellSamples().each{ processImage(user_client, it.getImage(), ilastik_project, ilastik_project_type, @@ -468,7 +470,7 @@ def processSingleWell(Client user_client, WellWrapper well_wrp, headless_mode, debug, tool_version, use_existing, final_object, rescue, ilastik_label_BG, probability_threshold_BG, - keep_only_largest) + keep_only_largest, segmentation_method) } } @@ -483,7 +485,7 @@ def processImage(Client user_client, ImageWrapper image_wrp, Boolean headless_mode, Boolean debug, String tool_version, Boolean use_existing, String final_object, Boolean rescue, Integer ilastik_label_BG, Double probability_threshold_BG, - Boolean keep_only_largest) { + Boolean keep_only_largest, String segmentation_method) { IJ.run("Close All", "") IJ.run("Clear Results") @@ -596,96 +598,105 @@ def processImage(Client user_client, ImageWrapper image_wrp, } if (!use_existing) { // We compute the segmentation - File output_path = new File (output_directory, image_basename+"_ilastik_" + ilastik_project_short_name + "_output.tif" ) - ImagePlus predictions_imp - FileSaver fs - if(output_path.exists()) { - println "USING EXISTING ILASTIK OUTPUT" - predictions_imp = IJ.openImage( output_path.toString() ) - } else { - /** - * ilastik - */ - println "Starting ilastik" - - // get ilastik predictions for each time point of the Time-lapse but all at the same time - ImagePlus ilastik_input_original = new Duplicator().run(imp, ilastik_input_ch, ilastik_input_ch, 1, 1, 1, nT); - - ImagePlus gb_imp = ilastik_input_original.duplicate() - IJ.run(gb_imp, "Gaussian Blur...", "sigma=100 stack") - ImagePlus ilastik_input = ImageCalculator.run(ilastik_input_original, gb_imp, "Divide create 32-bit stack") - if (!headless_mode) {ilastik_input.show()} - // can't work without displaying image - // IJ.run("Run Pixel Classification Prediction", "projectfilename="+ilastik_project+" inputimage="+ilastik_input.getTitle()+" pixelclassificationtype=Probabilities"); - // - // to use in headless_mode more we need to use a commandservice - def predictions_imgPlus - if (ilastik_project_type == "Regular") { - predictions_imgPlus = cmds.run( IlastikPixelClassificationCommand.class, false, - 'inputImage', ilastik_input, - 'projectFileName', ilastik_project, - 'pixelClassificationType', "Probabilities").get().getOutput("predictions") + if (segmentation_method == "ilastik") { + File output_path = new File (output_directory, image_basename+"_ilastik_" + ilastik_project_short_name + "_output.tif" ) + ImagePlus predictions_imp + FileSaver fs + if(output_path.exists()) { + println "USING EXISTING ILASTIK OUTPUT" + predictions_imp = IJ.openImage( output_path.toString() ) } else { - predictions_imgPlus = cmds.run( IlastikAutoContextCommand.class, false, - 'inputImage', ilastik_input, - 'projectFileName', ilastik_project, - 'AutocontextPredictionType', "Probabilities").get().getOutput("predictions") - } - // to convert the result to ImagePlus : https://gist.github.com/GenevieveBuckley/460d0abc7c1b13eee983187b955330ba - predictions_imp = ImageJFunctions.wrap(predictions_imgPlus, "predictions") + /** + * ilastik + */ + println "Starting ilastik" + + // get ilastik predictions for each time point of the Time-lapse but all at the same time + ImagePlus ilastik_input_original = new Duplicator().run(imp, ilastik_input_ch, ilastik_input_ch, 1, 1, 1, nT); + + ImagePlus gb_imp = ilastik_input_original.duplicate() + IJ.run(gb_imp, "Gaussian Blur...", "sigma=100 stack") + ImagePlus ilastik_input = ImageCalculator.run(ilastik_input_original, gb_imp, "Divide create 32-bit stack") + if (!headless_mode) {ilastik_input.show()} + // can't work without displaying image + // IJ.run("Run Pixel Classification Prediction", "projectfilename="+ilastik_project+" inputimage="+ilastik_input.getTitle()+" pixelclassificationtype=Probabilities"); + // + // to use in headless_mode more we need to use a commandservice + def predictions_imgPlus + if (ilastik_project_type == "Regular") { + predictions_imgPlus = cmds.run( IlastikPixelClassificationCommand.class, false, + 'inputImage', ilastik_input, + 'projectFileName', ilastik_project, + 'pixelClassificationType', "Probabilities").get().getOutput("predictions") + } else { + predictions_imgPlus = cmds.run( IlastikAutoContextCommand.class, false, + 'inputImage', ilastik_input, + 'projectFileName', ilastik_project, + 'AutocontextPredictionType', "Probabilities").get().getOutput("predictions") + } + // to convert the result to ImagePlus : https://gist.github.com/GenevieveBuckley/460d0abc7c1b13eee983187b955330ba + predictions_imp = ImageJFunctions.wrap(predictions_imgPlus, "predictions") - predictions_imp.setTitle("ilastik_output") + predictions_imp.setTitle("ilastik_output") - // save file - fs = new FileSaver(predictions_imp) - fs.saveAsTiff(output_path.toString() ) - } - if (!headless_mode) { predictions_imp.show() } + // save file + fs = new FileSaver(predictions_imp) + fs.saveAsTiff(output_path.toString() ) + } + if (!headless_mode) { predictions_imp.show() } - /** - * From the "ilastik predictions of the Time-lapse" do segmentation and cleaning - */ + /** + * From the "ilastik predictions of the Time-lapse" do segmentation and cleaning + */ - // Get a stack of ROI for background: - if (ilastik_label_BG != 0) { - ImagePlus mask_imp_BG = new Duplicator().run(predictions_imp, ilastik_label_BG, ilastik_label_BG, 1, 1, 1, nT) - // Apply threshold: - IJ.setThreshold(mask_imp_BG, probability_threshold_BG, 100.0000) - Prefs.blackBackground = true - IJ.run(mask_imp_BG, "Convert to Mask", "method=Default background=Dark black") - if (!headless_mode) { mask_imp_BG.show() } - IJ.run(mask_imp_BG, "Analyze Particles...", "stack show=Overlay") - Overlay ov_BG = mask_imp_BG.getOverlay() - Overlay ov_BG_Combined = new Overlay() - for (int t=1;t<=nT;t++) { - // Don't ask me why we need to refer to Z pos and not T/Frame - ArrayList all_rois_inT = ov_BG.findAll{ roi -> roi.getZPosition() == t} - println "There are " + all_rois_inT.size() + " in time " + t - if (all_rois_inT.size() > 0) { - ShapeRoi current_roi = new ShapeRoi(all_rois_inT[0] as Roi) - for (i = 1; i < all_rois_inT.size(); i++) { - current_roi = current_roi.or(new ShapeRoi(all_rois_inT[i] as Roi)) + // Get a stack of ROI for background: + if (ilastik_label_BG != 0) { + ImagePlus mask_imp_BG = new Duplicator().run(predictions_imp, ilastik_label_BG, ilastik_label_BG, 1, 1, 1, nT) + // Apply threshold: + IJ.setThreshold(mask_imp_BG, probability_threshold_BG, 100.0000) + Prefs.blackBackground = true + IJ.run(mask_imp_BG, "Convert to Mask", "method=Default background=Dark black") + if (!headless_mode) { mask_imp_BG.show() } + IJ.run(mask_imp_BG, "Analyze Particles...", "stack show=Overlay") + Overlay ov_BG = mask_imp_BG.getOverlay() + Overlay ov_BG_Combined = new Overlay() + for (int t=1;t<=nT;t++) { + // Don't ask me why we need to refer to Z pos and not T/Frame + ArrayList all_rois_inT = ov_BG.findAll{ roi -> roi.getZPosition() == t} + println "There are " + all_rois_inT.size() + " in time " + t + if (all_rois_inT.size() > 0) { + ShapeRoi current_roi = new ShapeRoi(all_rois_inT[0] as Roi) + for (i = 1; i < all_rois_inT.size(); i++) { + current_roi = current_roi.or(new ShapeRoi(all_rois_inT[i] as Roi)) + } + // Update the position before adding to the ov_BG_Combined + current_roi.setPosition( ilastik_input_ch, 1, t) + current_roi.setName("Background_t" + t) + ov_BG_Combined.add(current_roi) } - // Update the position before adding to the ov_BG_Combined - current_roi.setPosition( ilastik_input_ch, 1, t) - current_roi.setName("Background_t" + t) - ov_BG_Combined.add(current_roi) } + IJ.run("Clear Results") + println "Store " + ov_BG_Combined.size() + " BG ROIs on OMERO" + // Save ROIs to omero + robustlysaveROIs(image_wrp, user_client, ROIWrapper.fromImageJ(ov_BG_Combined as List)) } - IJ.run("Clear Results") - println "Store " + ov_BG_Combined.size() + " BG ROIs on OMERO" - // Save ROIs to omero - robustlysaveROIs(image_wrp, user_client, ROIWrapper.fromImageJ(ov_BG_Combined as List)) - } - // Get only the channel for the gastruloid/background prediction - mask_imp = new Duplicator().run(predictions_imp, ilastik_label_OI, ilastik_label_OI, 1, 1, 1, nT); + // Get only the channel for the gastruloid/background prediction + mask_imp = new Duplicator().run(predictions_imp, ilastik_label_OI, ilastik_label_OI, 1, 1, 1, nT); + + // Apply threshold: + IJ.setThreshold(mask_imp, probability_threshold, 100.0000); + Prefs.blackBackground = true; + IJ.run(mask_imp, "Convert to Mask", "method=Default background=Dark black"); + + } else { + // Get only the channel with bright field + mask_imp = new Duplicator().run(imp, ilastik_input_ch, ilastik_input_ch, 1, 1, 1, nT); + // Run convert to mask + (new Thresholder()).convertStackToBinary(mask_imp); + } // This title will appear in the result table mask_imp.setTitle(image_basename) - // Apply threshold: - IJ.setThreshold(mask_imp, probability_threshold, 100.0000); - Prefs.blackBackground = true; - IJ.run(mask_imp, "Convert to Mask", "method=Default background=Dark black"); if (!headless_mode) { mask_imp.show() } // clean the mask a bit @@ -775,8 +786,13 @@ def processImage(Client user_client, ImageWrapper image_wrp, rt.setValue("Unit", row, scale_unit) rt.setValue("Date", row, now) rt.setValue("Version", row, tool_version) - rt.setValue("IlastikProject", row, ilastik_project_short_name) - rt.setValue("ProbabilityThreshold", row, probability_threshold) + if (segmentation_method == "ilastik") { + rt.setValue("IlastikProject", row, ilastik_project_short_name) + rt.setValue("ProbabilityThreshold", row, probability_threshold) + } else { + rt.setValue("IlastikProject", row, "NA") + rt.setValue("ProbabilityThreshold", row, "NA") + } rt.setValue("MinSizeParticle", row, min_size_particle) rt.setValue("MinDiameter", row, minimum_diameter) rt.setValue("ClosenessTolerance", row, closeness_tolerance) @@ -1080,7 +1096,7 @@ def processImage(Client user_client, ImageWrapper image_wrp, // In simple-omero-client // Strings that can be converted to double are stored in double // In order to build the super_table, tool_version should stay String -String tool_version = "Phase_v20230728" +String tool_version = "White_v20231220" // User set variables @@ -1095,6 +1111,7 @@ String tool_version = "Phase_v20230728" #@ String(visibility=MESSAGE, value="Parameters for segmentation/ROI", required=false) msg2 #@ Boolean(label="Use existing segmentation (values below in the section will be ignored)") use_existing +#@ String(label="Segmentation Method", choices={"convert_to_mask","ilastik"}) segmentation_method #@ Boolean(label="Run in rescue mode
(only segment images without tables)", value=false) rescue #@ File(label="Ilastik project") ilastik_project #@ String(label="Ilastik project short name") ilastik_project_short_name @@ -1206,7 +1223,7 @@ if (user_client.isConnected()) { headless_mode, debug, tool_version, use_existing, "image", rescue, ilastik_label_BG, probability_threshold_BG, - keep_only_largest) + keep_only_largest, segmentation_method) break case "dataset": DatasetWrapper dataset_wrp = robustlyGetOne(id, "dataset", user_client) @@ -1233,7 +1250,7 @@ if (user_client.isConnected()) { headless_mode, debug, tool_version, use_existing, "dataset", rescue, ilastik_label_BG, probability_threshold_BG, - keep_only_largest) + keep_only_largest, segmentation_method) // upload the table on OMERO super_table.setName(table_name + "_global") robustlyAddAndReplaceTable(dataset_wrp, user_client, super_table) @@ -1263,7 +1280,7 @@ if (user_client.isConnected()) { headless_mode, debug, tool_version, use_existing, "well", rescue, ilastik_label_BG, probability_threshold_BG, - keep_only_largest) + keep_only_largest, segmentation_method) // upload the table on OMERO super_table.setName(table_name + "_global") robustlyAddAndReplaceTable(well_wrp, user_client, super_table) @@ -1293,7 +1310,7 @@ if (user_client.isConnected()) { headless_mode, debug, tool_version, use_existing, "plate", rescue, ilastik_label_BG, probability_threshold_BG, - keep_only_largest) + keep_only_largest, segmentation_method) // upload the table on OMERO super_table.setName(table_name + "_global") robustlyAddAndReplaceTable(plate_wrp, user_client, super_table) diff --git a/tools/omero_hyperstack_to_gastruloid_measurements/README.md b/tools/omero_hyperstack_to_gastruloid_measurements/README.md new file mode 100644 index 0000000..a51999e --- /dev/null +++ b/tools/omero_hyperstack_to_gastruloid_measurements/README.md @@ -0,0 +1,35 @@ +# OMERO hyperstack to gastruloid measurements + +## CHANGELOG + +### 20231220 + +- Add a new parameter: segmentation_method which can be 'ilastik' or 'convert_to_mask'. If 'convert_to_mask' is chosen, it does an autothreshold. +- The tool_version has been changed from Phase to White + +### 20230728 + +- Add a new parameter: keep_only_largest which allows to keep only the largest ROI for each stack + +### 20230727 + +- Add new parameters (ilastik_label_BG and probability_threshold_BG) to be able to generate a ROI for background. +- Add XCentroid and YCentroid to the result table + +### 20230628 + +- Change RoiWrapper to ROIWrapper + +### 20230623 + +- Be more robust to OMERO reboot: + - 'rescue' allows to only process images which does not have ROIs and tables and generate final table + - When making a query to omero repeat it after 0 minutes if it fails and again with 10, 60, 360, 600. + +### 20230405 + +- New parameter 'use_existing' allows to recompute only the spine + +### 20230324 + +First release diff --git a/tools/omero_hyperstack_to_gastruloid_measurements/omero_hyperstack_to_gastruloid_measurements.xml b/tools/omero_hyperstack_to_gastruloid_measurements/omero_hyperstack_to_gastruloid_measurements.xml index 575ba0c..8ae232b 100644 --- a/tools/omero_hyperstack_to_gastruloid_measurements/omero_hyperstack_to_gastruloid_measurements.xml +++ b/tools/omero_hyperstack_to_gastruloid_measurements/omero_hyperstack_to_gastruloid_measurements.xml @@ -1,26 +1,43 @@ - 20230728 + 20231220 - - - - - - - - - - - + + + + - - - + + + + + + + + + + + + + + + + + + + + + + - - - + + + + +
+ + +
@@ -46,9 +63,9 @@ echo "OMERO connection credentials are empty. Set your credentials via: User -> Preferences -> Manage Information" 1>&2 && exit 1 && #end if - #if str($mode.use_existing) == "false": - #set $ilastik_project_file = str($mode.ilastik_project) - #set $ilastik_project_name = str($mode.ilastik_project.name) + #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" @@ -58,7 +75,7 @@ ## 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="${omero_object.omero_id}",use_existing="${mode.use_existing}",ilastik_project="$ilastik_project_file",ilastik_project_short_name="$ilastik_project_name",ilastik_project_type="${mode.ilastik_project_type}",ilastik_label_OI="${mode.ilastik_label_OI}",probability_threshold="${mode.probability_threshold}",radius_median="${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="${mode.background.ilastik_label_BG}",probability_threshold_BG="${mode.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="${mode.min_size_particle}",get_spine="true",minimum_diameter="${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 ]]> @@ -111,18 +128,21 @@ $password - - - +
+ + + + +
+ + +
+
+ -
- - -
- @@ -133,18 +153,18 @@ $password - + - + keep_intermediate - + - + - keep_intermediate and mode['use_existing'] == "false" + keep_intermediate and mode['use_ilastik']['segmentation_method'] == "ilastik" From 24dea9d07e431fcb36510e337c83b8c58e4eec6f Mon Sep 17 00:00:00 2001 From: Lucille Delisle Date: Wed, 20 Dec 2023 20:58:51 +0100 Subject: [PATCH 2/2] fix url --- .../1-omero_timelapse_image_to_measurements_phase.groovy | 2 +- .../omero_hyperstack_to_gastruloid_measurements.xml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/tools/omero_hyperstack_to_gastruloid_measurements/1-omero_timelapse_image_to_measurements_phase.groovy b/tools/omero_hyperstack_to_gastruloid_measurements/1-omero_timelapse_image_to_measurements_phase.groovy index d0c5078..12a48c4 100644 --- a/tools/omero_hyperstack_to_gastruloid_measurements/1-omero_timelapse_image_to_measurements_phase.groovy +++ b/tools/omero_hyperstack_to_gastruloid_measurements/1-omero_timelapse_image_to_measurements_phase.groovy @@ -3,7 +3,7 @@ // 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/main/Fiji +// https://github.com/BIOP/OMERO-scripts/tree/025047955b5c1265e1a93b259c1de4600d00f107/Fiji // Last modification: 2023-12-20 diff --git a/tools/omero_hyperstack_to_gastruloid_measurements/omero_hyperstack_to_gastruloid_measurements.xml b/tools/omero_hyperstack_to_gastruloid_measurements/omero_hyperstack_to_gastruloid_measurements.xml index 8ae232b..7c81b85 100644 --- a/tools/omero_hyperstack_to_gastruloid_measurements/omero_hyperstack_to_gastruloid_measurements.xml +++ b/tools/omero_hyperstack_to_gastruloid_measurements/omero_hyperstack_to_gastruloid_measurements.xml @@ -184,7 +184,7 @@ License text:: // 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/main/Fiji + // https://github.com/BIOP/OMERO-scripts/tree/025047955b5c1265e1a93b259c1de4600d00f107/Fiji /* * = COPYRIGHT =