lacan
/ lutToIntensity.ijm
Last active
July 24, 2019 01:12
Reconvert color coded image to intensity based on color scale. #ImageJ #Fiji #Macro
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| /* | |
| * 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 24, 2024 12:27
Extract multi-series file and resave as TIFF stacks or slices #Fiji #ImageJ #Macro #BIOP
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| /* | |
| * 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
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| /* | |
| * 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
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| // @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
November 30, 2018 11:45
[Stitching with Flatfield Correction] Takes a folder as input and processed all multiseries files there using a provided flatfield file #Beanshell #Stitching #Fiji #ImageJ
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| //@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
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| /* | |
| * 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
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| /* | |
| * 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
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| //@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
October 22, 2020 10:14
[Parallel Histogram Matching for Stacks] #Groovy #Fiji #ImageJ
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| //@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
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| /** | |
| * 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/ |