romainGuiet
/ BIOPLib.ijm
Last active
August 29, 2015 14:11
A library of macro functions usefull for ActionBars (created using the ActionBar plugin ). Made at EPFL, BIOP, Olivier Burri, Romain Guiet.
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| // BIOP Functions Library v1.0 | |
| /* | |
| * Returns the name of the parameters window, as we cannot use global variables, | |
| * we just define a function that can act as a global variable | |
| */ | |
| function getWinTitle() { | |
| win_title= toolName(); | |
| // If something is already open, keep it as-is. | |
| if(!isOpen(win_title)) { |
romainGuiet
/ Temporal-Color_Code_BIOP.ijm
Created
May 20, 2016 09:23
A lightly modified version of Fiji.app\plugins\Scripts\Image\Hyperstacks\Temporal-Color_Code.ijm so it stops before projection, so you keep a colored stack
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| /* | |
| ************* Temporal-Color Coder ******************************* | |
| Color code the temporal changes. | |
| Kota Miura (miura@embl.de) | |
| Centre for Molecular and Cellular Imaging, EMBL Heidelberg, Germany | |
| If you publish a paper using this macro, please acknowledge. |
romainGuiet
/ rotateLineAroundCenter.ijm
Created
March 14, 2019 08:58
ImageJ macro language : Around a fixed point, get the x,y corrdinates of the points rotating around the center at a defined distance
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| /* | |
| * Use of the custom function rotateLine(...) | |
| * Around a fixed point, get the x,y corrdinates | |
| * of the points rotating around the Center at a defined distance | |
| * | |
| */ | |
| selectWindow("blobs.gif"); | |
| // Center Point coordinates |
romainGuiet
/ multi_DoG.ijm
Created
March 30, 2019 08:41
An ImageJ macro language script to perform multi_DoG
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| title = getTitle; | |
| close("\\Others"); | |
| roiManager("Reset"); | |
| sigma1 = newArray(1,2,3,4,5,10); | |
| for (i = 0 ; i < lengthOf(sigma1) ; i++) { | |
| selectWindow(title); | |
| run("Duplicate...", "title=gb1"); | |
| run("Gaussian Blur...", "sigma="+sigma1[i]); |
romainGuiet
/ make_ROIs_from_labels.ijm
Created
July 3, 2019 09:23
an ImageJ macro to make ROIs from image with labels
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| roiManager("reset"); | |
| getStatistics(area, mean, min, max, std, histogram); | |
| for (i = 1; i <= max; i++) { | |
| setThreshold(i, i); | |
| run("Create Selection"); | |
| Roi.setName(IJ.pad(i,6)) | |
| roiManager("Add"); | |
| } |
romainGuiet
/ unzip.py
Last active
October 29, 2019 13:32
Export zip file content in current working directory
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| archive_name = "models.zip" | |
| import os | |
| import zipfile | |
| # retrieve the pat of the current directory (bash command uses !...) | |
| path=!pwd | |
| path = path[0] | |
| # create the archive path using path and archive_name |
romainGuiet
/ postprocessing.txt
Created
December 3, 2019 14:08
Postprocessing macro for DeepImageJ using StarDist model
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| name=getTitle(); | |
| run("Make Substack...", "channels=1"); | |
| rename("Predicted object probability"); | |
| proba_ID = getImageID(); | |
| run("Fire"); | |
| selectWindow(name); | |
| run("Make Substack...", "channels=2-33"); |
romainGuiet
/ qps-export_annotations_as_ijROIs.groovy
Last active
December 20, 2019 11:31
QuPath script (qps) to export the image annotations as a ROIset.zip in a '/ROI Sets' folder. The ROIset.zip saving/naming convention respect the ImageJ's BIOPLib.ijm (from PTBIOP update site).
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| // = CODE DESCRIPTION = | |
| // Image annotations are saved as a ROIset.zip in a '/ROI Sets' folder, so they can be re-open in Image-j | |
| // The ROIset.zip saving/naming convention respect the ImageJ's BIOPLib.ijm (from PTBIOP update site). | |
| // | |
| // == INPUTS == | |
| // A QuPath project, with annotations. | |
| // | |
| // == OUTPUTS == | |
| // The annotations are saved as a ROIset.zip in a '/ROI Sets' folder, | |
| // |
romainGuiet
/ LabelImageToRoiManager.groovy
Created
January 14, 2020 10:09
Add ROIs to ImageJ roiManager from an image with labels.
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| // adapted from https://gist.github.com/NicoKiaru/ae00117cd6d33fea500d2867a5e669d9 | |
| // | |
| // = CODE DESCRIPTION = | |
| // Add ROIs to ImageJ roiManager from an image with labels. | |
| // | |
| // == INPUTS == | |
| // A label image, grey or RGB. | |
| // | |
| // == OUTPUTS == | |
| // Rois in ImageJ roiManager. |
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 | |
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