lacan

#@ File idFile ( label="'Index.idx.xml' file" )
#@ File saveFolder ( label="Save Folder", style="directory" )

// Define stitching parameters. Nothing here is flexible but feel free to try
def params = new  mpicbg.stitching.StitchingParameters()
params.channel1 = 0;
params.channel2 = 0;
params.timeSelect = 0;
params.checkPeaks = 5;
params.fusionMethod = 0

lacan

#@ File image_dir1 ( label="First directory", style="directory" )
#@ File image_dir2 ( label="Second directory", style="directory" )
#@ Boolean save_plot ( label="Save plot?" )
#@ Boolean save_data ( label="Save Data points?" )
#@ String threshold_method (label="Threshold method", choices={"Fixed 1/7", "Half-bit", "Three sigma"})


import ch.epfl.biop.frc.FRC
import ch.epfl.biop.frc.FRC.ThresholdMethod
import ij.IJ

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// Reference: https://forum.image.sc/t/basic-macro-help-rois-to-svg/7861/3
#@ File svgFile ("style=save")

svg = "<?xml version=\"1.0\" ?><svg xmlns='http://www.w3.org/2000/svg' xmlns:xlink='http://www.w3.org/1999/xlink' xmlns:jfreesvg='http://www.jfree.org/jfreesvg/svg' width='"+getWidth()+"' height='"+getHeight()+"'>\n";
n = roiManager("count");
for (j = 0; j < n; j++){

	roiManager("select", j);
	getSelectionCoordinates(x, y);
	text = "<path d='m";

lacan

/**
 * Reduce Detection size to create new cell objects and add measurements
 * @author Olivier Burri
 * @date 20240212
 */
 
// By how much should the existing detections be reduced to create the new "nucleus"
def erosionDistancePx = -5

// Should the intensities be measured on a downsampled image?

lacan

// Resave image as a pyramidal ome.tiff at the desired downsample and bit depth
// @author Olivier Burri
// 16-bit magic trick inspired from
// https://forum.image.sc/t/software-recommendations-converting-a-32bit-ome-tiff-to-an-8bit-ome-tiff/43043
// But did not use scaling parameter

//  ****** PARAMETERS *********

// Output downsample (1 for full-resolution)
def outputDownsample = 1

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// DISCLAIMER: The algorithm was taken from a ChatGPT prompt "What is the Groovy implementation of the 2D Relative Neighborhood Graph Algorithm"
// It is merey an alpha version of the code and has not been thorougly tested at all, nor has the code been optimized. 
// The original prompt has been slightly modifided to make better use of ImageJ methods to display the graph


// Create a list of points for testing
def rand = new Random()
// Or to make it reproducible
//def rand = new Random( 1000 )

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/*
 * Update QuPath URIs
 * After the migration of our EPFL servers from svfasX to sv-nas1.rcp, some projects fail to open in a timely manner, 
 * especially under Windows when  the full path to the server is used (instead of a networked drive). 
 * The reason seems to be that QuPath is waiting for a response from the server, and the timeouts are long, so it takes a 
 * really long time before the "Update URIs" window pops up
 * 
 * This script aims to assist in fixing that by at least changing the host name (svfasX) to a valid host (sv-nas1.rcp)
 * that way, QuPath will immediately either find or fail to find the file, restoring normal behavior
 * 

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// Example creating a dialog to run tasks in a script. 
// We need to discern between headless and non-headless manually so far
// @author Olivier Burri
//

import qupath.lib.plugins.CommandLinePluginRunner
import qupath.lib.gui.PluginRunnerFX

// Define the runner, in this case we will not use it but it is quite powerful
def runner

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// Define Clusters based on distance and from cells with different classifications
// This script works for images wehre multiple cell signals are segmented as detections
// The detections must be children of annotations objects
// And then a clustering step is used to get multi-classification cells
// The clustering results are provided as circles withg name "Cluster" so you can filter from the original detections
// Works in QuPAth 0.4.3
//
// @author Olivier Burri
// @date 20230425

lacan

#@File originalDir (label="Directory with original VSI Files", style="directory")
#@File csvFile (label="CSV File with full VSI file path in columns 1 and new name in column 2")
#@String sep (label="CSV separator", value=";")

/*
 * Rename VSI images based on CSV reference file 
 */

println sep
def csvImages = csvFile.readLines()*.split(sep)