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 | |
| * [email protected] | |
| * September 2020 |
romainGuiet
/ ilastik4fiji.ijm
Created
November 6, 2020 10:13
a minimal example of ilastik called from fiji. https://go.epfl.ch/ilastik-tuto-2020 #BIOP #fiji #macro #ilastik
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| #@ File projectFile | |
| imageName = getTitle(); | |
| run("Run Pixel Classification Prediction", "projectfilename="+projectFile+ | |
| " inputimage=["+imageName+"]"+ | |
| " pixelclassificationtype=Probabilities"); | |
romainGuiet
/ closeOthers.groovy
Last active
August 9, 2024 11:19
groovy command equivalent to 'close("\\others")' in macro language. #BIOP #Groovy #Macro
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| // https://forum.image.sc/t/macro-function-close-others-in-groovy/44630 | |
| // Using ID as proposed by @imagejan | |
| import ij.WindowManager | |
| #@ ImagePlus imp | |
| WindowManager.getIDList() | |
| .findAll{ it != imp.getID() } | |
| .each{ WindowManager.getImage(it).close() } | |
| null // suppress result processing by SciJava |
romainGuiet
/ ijs-export_lif_zprojAvailable.groovy
Last active
November 15, 2024 15:56
A groovy script usable in FIJI to export images of a lif file (should work with other bioformats supported format). User can specify the series to export using comma (1,2,3) or a range using dash (1-5) , or nothing to export all series #BIOP #FIJI #groovy #export #bioformats
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| #@ File image_path | |
| #@ String seriesNbr | |
| #@ String (choices={"max","avg","sum","none"}) zProj | |
| import org.apache.commons.io.FilenameUtils | |
| import ij.* | |
| import ij.plugin.ZProjector | |
| import ij.io.FileSaver |
romainGuiet
/ qps-export_3D_labels.groovy
Last active
June 11, 2020 09:41
a prototype groovy script to export 3D labels from QuPath annotation
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| /* QuPath-Script to export annotations to label tif images (e.g. to be used for stardist) | |
| Use "Run for project" to export annotations for all images within a QuPath project | |
| Afterwards both images and mask tiffs will be stored in the project subfolder | |
| ground_truth | |
| ├── images | |
| └── masks | |