romainGuiet
/ getImagePlusInfo.groovy
Created
August 19, 2019 07:51
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| import ij.* | |
| import ij.plugin.Duplicator | |
| import ij.io.FileSaver | |
| /** | |
| * | |
| * Here is a groovy script which: | |
| * - Gets information about the current ImagePlus File (via imp.getOriginalFileInfo()), | |
| * - Retrieves its directory | |
| * - Creates an output subfolder |
romainGuiet
/ BIOP-userProject.ijm
Last active
June 16, 2021 14:26
A ImageJ macro to create a standardized "User Project" folder. #BIOP #FIJI #Macro #UserProject
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| #@File(label="Please select an UserName-Lab", style="directory") selected_dir | |
| #@String() projectName | |
| /* | |
| * Macro to create a folder accordingly to BIOP template. | |
| * | |
| * | |
| * | |
| * git need to be installed |
lacan
/ Export Annotations For Stardist.groovy
Last active
July 30, 2023 14:32
[QuPath Script To Export Annotations For Stardist] this script will take rectangular annotations in QuPath and export them and their containing objects as images and masks for deep neural netowrk training #qupath #stardist #BIOP
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| /* | |
| // ABOUT | |
| Exports Annotations for StarDist (Or other Deep Learning frameworks) | |
| // INPUTS | |
| You need rectangular annotations that have classes "Training" and "Validation" | |
| After you have placed these annotations, lock them and start drawing the objects inside | |
| // OUTPUTS | |
| ---------- |
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 |
NicoKiaru
/ OpenOMERO.groovy
Last active
January 24, 2025 16:21
Open an OMERO dataset into Fiji with caching #BIOP #Fiji
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| // Open a URL from OMERO with caching into Fiji as an ImagePlus | |
| // Requires PTBIOP and OMERO 5.5 5.6 update site | |
| // Written by Nicolas Chiaruttini on 24th Jan 2025 | |
| // Try https://omero-tim.gerbi-gmb.de/webclient/?show=image-104300 with: | |
| // login: read-tim | |
| // passwd: read-tim | |
| #@CommandService cs | |
| #@String(label="omero url") url | |
| #@SourceAndConverterService source_service |