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| #@ ImagePlus imp | |
| #@ Double tolerance | |
| nT = imp.getNFrames() | |
| imp.getStack(). | |
| means_vals = (1..nT).collect{ | |
| imp.setT(it) | |
| return imp.getStatistics().mean | |
| } |
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| /* = CODE DESCRIPTION = | |
| * This QuPath script fills thae image Annotations objects with circular detections objects of a user defined diameter. | |
| * In combination with "Measure > Show measurements maps" it can be helpfull to quickly create meaningful heatmaps. | |
| * | |
| * == INPUTS == | |
| * Annotation(s) and RegionOfInterest diamater (in microns) | |
| * | |
| * == OUTPUTS == | |
| * circular detections objects of a user defined diameter | |
| * |
romainGuiet
/ RUN_mulitpleParam_Cellpose.groovy
Created
March 16, 2022 13:48
A groovy script to batch test param for cellpose
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| #@File file_path | |
| IJ.run("Close All", ""); | |
| // the folder containing the lif | |
| dir = file_path.getParent() | |
| // a subfolder to save images | |
| output_dir = new File( dir ,"outputRom1PC") | |
| output_dir.mkdir() |
romainGuiet
/ make_3D_labels.groovy
Created
October 27, 2021 13:53
Convert a Labels image to Measurements image (requires morpholibJ)
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| #@ImagePlus imp // imp should be a 3D label image | |
| #@String stat_name // morpholibJ output table after Analyze Regions 3D | |
| // using morpholibJ , update site : IJPB-plugins | |
| IJ.run("Analyze Regions 3D", "voxel_count volume surface_area mean_breadth sphericity euler_number bounding_box centroid equivalent_ellipsoid ellipsoid_elongations max._inscribed surface_area_method=[Crofton (13 dirs.)] euler_connectivity=6"); | |
| // Duplicate the imp and make it 32-bit | |
| imp_label = imp.duplicate(); | |
| IJ.run(imp_label, "32-bit", ""); |
romainGuiet
/ ROIsRings_DistanceMap.ijm
Last active
April 6, 2021 06:16
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| run("Close All"); | |
| roiManager("reset"); | |
| // ring thickness | |
| step = 10 ; | |
| // prepare a test image | |
| setForegroundColor(255, 255, 255); | |
| setBackgroundColor(0, 0, 0); | |
| newImage("Shape", "8-bit black", 512, 512, 1); | |
| makePolygon(258,122,171,192,115,272,167,430,232,350,229,302,289,338,324,300,329,236,411,160); |
romainGuiet
/ fake_StarDist3D.groovy
Created
February 5, 2021 12:22
a fake StarDist3D combining StarDist2D+TrackMate+LaRoME
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| #@File image_path | |
| #@RoiManager rm | |
| #@ CommandService command | |
| #@ Double (label="Nuclei Proba. Threshold", value=0.5) threshold_proba_nuc | |
| #@ Double (label="Nuclei min. intensity (A.U.)", value=10) minInt_nuc | |
| #@Integer (label="Max Frame Gap") frameGap | |
| #@Double (label="Linking Max Distance") linkDistance | |
| #@Integer (label="Gap Closing Max Distance") gapClosingDistance | |
| // authors : olvier.burri & romain.guiet (at) epfl.ch |
romainGuiet
/ test_optionDisableSmoothing.ijm
Created
January 15, 2021 07:47
For the review of the article (https://f1000research.com/articles/9-1380). A macro to test the option "disable smoothing" of the plugin "Process>Subtract Background..."
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| run("Close All"); | |
| run("Blobs (25K)"); | |
| img1 = getImageID(); | |
| run("Invert LUT"); | |
| run("32-bit"); | |
| rename("On_disableSmoothing"); | |
| run("Duplicate...", "title=Off_disableSmoothing"); | |
| img2 = getImageID(); |
romainGuiet
/ ijs-EasyXT-Filter_detectedSpots.groovy
Last active
December 18, 2020 06:28
An example script to show how to filter spots after the detection. #Fiji #EasyXT-Fiji #Imaris #BIOP
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| name_spots = "pinkySpots"; | |
| name_filtered_spots = name_spots+"-filtered"; | |
| rt = new ResultsTable() | |
| rt.reset() | |
| // Here teh script expect to find the demo.ims file in the folder Fiji>Plugins>BIOP | |
| def plugins_dir = IJ.getDirectory("plugins") | |
| def biop_dir = new File(plugins_dir , "BIOP") | |
| ims_name = "HeLa_H2B-mcherry_Tubline-EGFP_mitochondria-MitoTracker_reduced.ims" |
romainGuiet
/ image_fig.ijm
Last active
December 7, 2020 06:42
A imagej macro to create the image from Figure 3, https://f1000research.com/articles/9-1380/v1
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| oneOval = 1 ; | |
| //size_Array = newArray(1,5,10,20,50,100); | |
| size_Array = newArray(7,9,11,15,20,25,50); | |
| int_Array = newArray(5,10,20,50,100,150,250); | |
| Array.getStatistics(size_Array, size_Array_min, size_Array_max, size_Array_mean, size_Array_stdDev); | |
| //print(size_Array_max); |
romainGuiet
/ image_and_pointList_toXML.ijm
Created
November 18, 2020 14:16
#macro #xml #LabelImg #ZeroCostDL4Mic #BIOP
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| /* | |
| * Romain Guiet | |
| * EPFL | |
| * Nov 2020 | |
| * | |
| * adapted from : https://raw.githubusercontent.com/bvernay/ImageJ-Macros/master/xml_annotations_tools/roiTOXML.ijm | |
| * Bertrand Vernay | |
| * Imaging Centre IGBMC | |
| * vernayb@igbmc.fr | |
| * September 2020 |
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