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

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

// 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

// Save the whole Image

def downsample = 4

// Save the whole Image
def request = RegionRequest.createInstance( getCurrentServer(), downsample )

            
def imageData = getCurrentImageData()

lacan

// Create cytoplasm ROI before adding it to the Roi Manager?
def getcytoplasm = true


// START OF SCRIPT

// Use ImageJ's RoiManager
def rm = RoiManager.getInstance() == null ? new RoiManager() : RoiManager.getInstance()
rm,.reset()

lacan

// Export Rendered view of S1HL as open in QuPath with metadata tag  in file name
// Author: Olivier Burri
// originally for Julie Meystre, LNMC
// Date: 2022 03 11

// NOTE: Make sure that all settings are as you want them on a currently open image (Channels, hidden Pathclasses, Annotation names, ...) before you start, as your current display and layer settings will be applied to all image if you use "Run for Project"

def downsample = 5
def regionClass = "S1HL"
def metadataName = "Distance to midline"

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
 * 
 */

lacan

// You are a smart one
// But we did not share a solution to this code :)
// Here it is again just for you:

// You are a smart one
// But we did not share a solution to this code :)
// Here it is again just for you:

run("Set Measurements...", "area mean standard modal min limit display redirect=None decimal=3");