lacan

% 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 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

% 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

/**
 * Regularity Index Measurement
 * Author: Olivier Burri
 * Contact: http://biop.epfl.ch/INFO_Facility.html#staff
 * Affiliation: BioImaging & Optics Platform, EPFL School of Life Sciences
 * Date: 18 August 2015
 * License: CC BY http://creativecommons.org/licenses/by/4.0/
 * 
 * Description: Measures the regularity index from an ImageJ Voronoi diagram
 *

lacan

/*
* By Olivier Burri, BioImaging & Optics Platform EPFL
* June 2016
* Provided as-is from a request on the ImageJ Forum
* http://forum.imagej.net/t/dividing-circle-into-8-equal-areas/1995
*/

var count = 0;  // Variable to know which circle we are working on

// If you install this macro, it will be mapped to the F2 Key

lacan

/*
 * Simple bissection tool. By Olivier Burri at the BioImaging and Optics Platform
 * Provided as-is based on a request of the ImageJ Forum: http://forum.imagej.net/t/how-do-you-measure-the-angle-of-curvature-of-a-claw
 * 
 * Mouse listening code based on imageJ example
 * https://imagej.nih.gov/ij/macros//GetCursorLocDemo.txt
 * 
 * To install, use 'Plugins > Macros > Install...' and select this file
 * 
 * To run, create a line selection and press F2.

lacan

#@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

saveDir = getDirectory("Save Directory");
image = getTitle();
run("Grouped Z Project...", "projection=[Max Intensity] group=25");

groups = getTitle();
getDimensions(gx,gy,gc,gz,gt);
setBatchMode(true);
for(g=0;g<gt;g++) {
	selectImage(groups);
	setSlice(g+1);

lacan

/* 
 * 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

/*
 * 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
 */