lacan
/ lutToIntensity.ijm
Last active
July 24, 2019 01:12
Reconvert color coded image to intensity based on color scale. #ImageJ #Fiji #Macro
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| /* | |
| * Reconvert color LUT to intensity | |
| * Olivier BURRI | |
| * BioImaging and Optics Platform BIOP, EPFL | |
| * In reply to an ImageJ Forum Post http://forum.imagej.net/t/split-colored-height-map-of-moon-in-greyscale-images/ | |
| * Provided As-Is | |
| */ | |
| // Before running this macro, make sure that you have an image called LUT with the color scalebar separately |
lacan
/ Export_Images_Folder.ijm
Last active
February 2, 2025 20:59
Extract multi-series file and resave as TIFF stacks or slices #Fiji #ImageJ #Macro #BIOP
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| /* | |
| * Complex Format EXPORT MACRO | |
| * By Olivier Burri @ EPFL - SV - PTECH - BIOP | |
| * Given a folder, extracts all series inside all multi-file files with given extension in new folders | |
| * Last edit: 13.02.2017 | |
| */ | |
| ////////////////////// SET PARAMETERS ////////////////////// | |
| //////////////////////////////////////////////////////////// |
lacan
/ curvature_radius.bsh
Last active
October 13, 2022 15:18
Curvature radius simple calculation for ImageJ/fiji #Fiji #Beanshell #Curvature #ImageJ
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| /* | |
| * Simple script that takes a selection and computes the curvature radius for the whole perimeter of the shape. | |
| * | |
| * By Olivier Burri, | |
| * BioImaging and Optics Platform, BIOP | |
| * Ecole Polytechnique Fédérale de Lausanne (EPFL) | |
| * Last update: May 2017 | |
| * | |
| * | |
| */ |
lacan
/ Prune_Skeleton_Ends.bsh
Last active
October 22, 2020 09:30
[Prune Skeleton Ends] Script to prune skeletons endpoints whose branches are shorter than the specified distance #Beanshell #ImageJ #Fiji #Skeleton #BIOP
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| // @ImagePlus(label="Skeleton image", description="Binary image skeletonized with Skeletonize3D") image | |
| // @double(label="Length threshold", description="Minimum branch length to keep") threshold | |
| // @OUTPUT ImagePlus prunedImage | |
| import sc.fiji.analyzeSkeleton.AnalyzeSkeleton_; | |
| import sc.fiji.analyzeSkeleton.Edge; | |
| import sc.fiji.analyzeSkeleton.Point; | |
| import ij.IJ; | |
| // analyze skeleton |
lacan
/ Stitch_Correction.bsh
Last active
April 9, 2025 12:32
[Stitching with Flatfield Correction] Takes a folder as input and processed all multiseries files there using a provided flatfield file #Beanshell #Stitching #Fiji #ImageJ
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| //@File(label="Multiposition Files Directory",style="directory") image_directory | |
| //@String(value="Select a file for flat field correction or write none", visibility="MESSAGE") textFF | |
| //@File(label="Flatfield Correction File", value="none") ff_file | |
| //@int(label="Downsample Factor", style = "slider", min = "1", max = "16", stepSize = "1") downsample | |
| //@Boolean(label="Compute Overlap") is_compute | |
| //@String(label="Macro Mode",choices={"Fuse and display","Write to disk"}) output_type | |
| //@LogService log | |
| import ij.IJ; | |
| import loci.formats.ImageReader; |
lacan
/ Normalize_Line_Straighten.ijm
Last active
October 22, 2020 10:07
[Nomalize Line Profile] Normalizes line profiles by making use of the Straighten command followed by scaling #Macro #ImageJ #Fiji #BIOP
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| /* | |
| * Normalizes line profiles by making use of the Straighten command followed by scaling | |
| * By Olivier Burri, BioImaging And Optics Platform | |
| * In Response to http://forum.imagej.net/t/average-pixels-with-line-tool/6408?u=oburri | |
| * | |
| * OUTPUT is the values of the line profile as a results table | |
| * Column name is the image name. | |
| * the number of rows corresponds to the normalization length normLength | |
| */ |
lacan
/ get_Distances.ijm
Created
August 10, 2017 11:10
[Compute Distance Based on Edges] Determine Length of a rather homogeneous structure using Find Edges on graylevel image #Macro #ImageJ #Fiji
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| /* | |
| * Determine Length of a rather homogeneous structure using Find Edges on graylevel image | |
| * | |
| * using an iterative approach to end up having exactly two peaks on the | |
| * maximum finder. | |
| * | |
| * By Olivier Burri | |
| * BioImaging And Optics Platform. | |
| * | |
| * In response to http://forum.imagej.net/t/how-calculate-the-pixels-distance/6478?u=oburri |
lacan
/ Rescale_Images_Parallel.groovy
Last active
October 22, 2020 10:14
[Rescale images in XYZ Parallel] Resamples images in parallel #Fiji #ImageJ #Bioformats #Groovy
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| //@File (label="Series File") image_file | |
| //@Integer(label="XY Resampling") xy_resampling | |
| //@Integer (label="Z Step") z_step | |
| import loci.plugins.util.BFVirtualStack | |
| import loci.formats.ChannelSeparator | |
| import ij.ImagePlus | |
| import ij.IJ | |
| import groovyx.gpars.GParsExecutorsPool |
lacan
/ Histogram_Matching_Parallel.groovy
Last active
June 12, 2024 10:05
[Parallel Histogram Matching for Stacks] #Groovy #Fiji #ImageJ
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| //@File (label="Directory with file(s)", style="directory" ) theDir | |
| //@Integer (Label="Channel To Correct") ch_correct | |
| //@Boolean (label="Use Normalization Parameters Below") is_normalize | |
| //@Integer (Label="Minimum") the_min | |
| //@Integer (Label="Maximum") the_max | |
| /** | |
| * Image stack equalizer for image folder | |
| * | |
| * The purpose of this script is to use the histogram of the first slice of the first image |
lacan
/ find_delaunay_neighbors_distance_demo.ijm
Last active
December 8, 2018 10:00
[Neighbors from Delaunay] Find Average Neighbor Distance From Delaunay Triangulation Demo #ImageJ #Fiji #Macro
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| /** | |
| * Demo of using Delaunay triangulation to find average inter-neighbor distances | |
| * In reply to ImageJ forum post: | |
| * http://forum.imagej.net/t/measuring-distance-to-neigbours/10712 | |
| * | |
| * Olivier Burri, EPFL BIOP (BioImaging And Optics Platform) | |
| * May 1st 2018 | |
| * | |
| * Provided as-is under Creative Commons Attribution 4.0 International License | |
| * https://creativecommons.org/licenses/by/4.0/ |