lacan
/ new_results_table.ijm
Last active
June 16, 2017 10:20
Make a new table with only the bounding box and label informations #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
| /* | |
| * Make a new table with only the bounding box and label informations | |
| * Olivier BURRI, November 2016 | |
| * Provided as-is, based on a request on the ImageJ List | |
| * http://forum.imagej.net/t/creating-and-saving-a-custom-table-from-results/3285?u=oburri | |
| */ | |
| nR = nResults; | |
| label = newArray(nR); | |
| x1 = newArray(nR); |
lacan
/ batchColoc.m
Last active
June 16, 2017 10:39
Matlab Batch Coloc For Many Channels #Matlab #EasyXT #Coloc #Imaris
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
| % Get EasyXT at: | |
| % https://github.com/lacan/EasyXT | |
| % The very first time you run it, use | |
| % X = EasyXT('setup') | |
| % To tell the XTension where the Imaris Executable file is. | |
| % Disclaimer | |
| % This code is provided as-is and hopefully will be of some use to people | |
| % Olivier BURRI, Romain GUIET @ BIOP (EPFL - BioImaging & Optics Platform), July 2015 |
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
/ simpleKNN.py
Last active
March 16, 2018 20:56
2D K Nearest Neighbors Python script when we have a point selection in ImageJ #Fiji #Python #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
| #@ImagePlus imp | |
| #@Integer(label="Number of Neighbors") k | |
| #@Boolean(label="Give Each Neighbor's Distance") is_show_each | |
| ''' | |
| Simple 2D KNN script | |
| Olivier Burri, BioImaging & Optics Platform | |
| Ecole Polytechnique Fédérale de Lausanne | |
| July 12th 2016 |
lacan
/ batchChannelMath.m
Last active
July 27, 2018 16:48
Imaris Batch Channel Math with EasyXT #Imaris #EasyXT #Matlab
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
| % Example of looping through a folder to process a series of images. | |
| % In this case, perform channel math. | |
| % For convenience, this example uses EasyXT, but feel free to adapt it as needed. | |
| % Get EasyXT Here: http://lacan.github.io/EasyXT/ | |
| % The ChannelMath method is borrowed from the XTension with the same name, made by Bitplane. | |
| folder_name = uigetdir(); | |
| listing = dir(folder_name); |
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
/ 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/ |
lacan
/ points_to_curve_distance.ijm
Last active
March 29, 2019 01:13
Points To Curve Distance using Distance Map imageJ Macro #ImageJ #Macro #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
| /* | |
| * Distance of points to freehand line | |
| * using distance transform | |
| * Inspired by work from 2011 For Dr. Giuseppe Lo Sasso | |
| * | |
| * Olivier BURRI November 2016 | |
| * Provided as an example for a post on the ImageJ Forum | |
| * http://forum.imagej.net/t/quantifying-distance-of-multiple-points-from-a-freehand-line/3287 | |
| */ |
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
/ BigStitcher_Flip_Axes.groovy
Last active
October 28, 2019 08:02
[BigStitcher Flip Axes] Implements the Flip Axes Command from BigStitcher in a Macro Recordable Way #SPIM #BigStitcher #Fiji #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
| /** | |
| * Implements the Flip Axes Command from BigStitcher | |
| * | |
| * Recommendation is to place this file in | |
| * [FIJI Folder]/plugins/Scripts/Plugins/BigStitcher/Custom Scripts | |
| * | |
| * By Olivier Burri for Kai Schleicher, | |
| * https://forum.image.sc/t/bigstitcher-flip-axes-in-headless-mode/30557?u=oburri | |
| * BSD 3 License | |
| * |
OlderNewer