lacan

/**
 * Calculate 1D Full Width at half Maximum of a single line or a series of lines added to the ROI Manager
 * Created by Olivier Burri and Romain Guiet, BioImaging & Optics Platform (BIOP)
 * Last Update: 2020.10.21
 * 
 * Due to the simple nature of this code, no copyright applies
 *
 * Installation 
 * ------------
 * From within Fiji Please use "Plugins > Macros > Install" and select this file

lacan

// 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

import java.awt.Color
import ij.process.ColorProcessor
import ij.process.AutoThresholder
import ij.plugin.filter.ThresholdToSelection
import ij.IJ

// modified from : 
// https://petebankhead.github.io/qupath/scripting/2018/03/08/script-imagej-to-qupath.html

// This scripts allow threholding of a color deconvoltuion channel ('DAB', 'Hematoxylin',...)

lacan

// This script was created for Anna Hamacher, as per an internal discussion on the ImageSC forum
// that stemmed from https://forum.image.sc/t/viewing-slide-scans-from-operetta-perkin-elmer-cls-as-overview-montage-images/52942/13?u=oburri
// Code by Olivier Burri, EPFL - SV - PTECH - BIOP
// Edited by Anna Hamacher
// Last edition: July 2022

#@ File dir (label="Images Folder", style="directory")
#@Integer downsample (label="Downsample Factor", value=1)
#@String z_projection_method (label = "Projection Type", choices = {"No Projection", "Average Intensity", "Max Intensity", "Min Intensity", "Sum Slices", "Standard Deviation", "Median"} )
#@File outputDir (label="Output directory", style="directory")

lacan

macro "Assess Bleaching [F2]" {
	// Measure Half time and relate it to number of frames
	run("Close All");
	// Get the contents of the clipboard as text
	text = String.paste;
	
	// Split the lines and then the rows so as to get the X and Y coordinates
	line = split(text, "\n");
	n = line.length;
	

lacan

/*
 * 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

// This workflow represents the end result that can be obtain by following Dr. Sara McArdle's "Running a complex project in QuPath" tutorial at https://www.youtube.com/watch?v=7AvuzAgHk5o
// @author Olivier Burri

// Prepare the image type
setImageType('FLUORESCENCE')

// Clean up the current image data, as we assume we will be starting from scratch
clearAllObjects()

// Directly create detections from a previously created pixel classifier called "Ck"

lacan

#@ File imagesDirectory (label="Directory with images", style="directory")
#@ String extension (label="Image extension", value="tif")
#@ String quPathExe (label="Path to QuPath Executable", value="C:/QuPath-0.3.2/QuPath-0.3.2 (console).exe")

import groovyx.gpars.GParsPool

def folder = imagesDirectory

def convertedFolder = new File( folder.getParent(), "converted")
convertedFolder.mkdirs()

lacan

#@ File saveLocation (label="Location of MIDI save file")

/**
 * Testing Spots to Sound using MIDI
 * Each hit is given a unique note based on some metric and intensity is related to volume
 * 
 * = AUTHOR INFORMATION =
 * Code written by Olivier Burri, EPFL - SV - PTECH - BIOP
 * for Samuel Vernon, McCabe Lab
 * 2022.08.23

lacan

/**
 * Use StarDist in TrackMate from the latest version and export results
 * Using a custom StarDist Model
 * Author: Olivier Burri, EPFL SV PTECH BIOP
 * Last Modification: March 2022
 * 
 * Due to the simple nature of this code, no copyright is applicable
 * 
 */