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#@ 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()

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#@ 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

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// Save the whole Image

def downsample = 4

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

            
def imageData = getCurrentImageData()

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// 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()

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// 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"

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/**
 * 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
 * 
 */

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// 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");

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

run("Split Channels");
selectWindow("C1-Edu+_RFP+_(2).tif")
run("Median...", "radius=5");
setAutoThreshold("Li dark");
run("Create Selection");

selectWindow("C2-Edu+_RFP+_(2).tif");
run("Restore Selection");

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/** 
 * Split Imaris Tracked Nuclei into separate ims files 
 * 
 * 
 * Author: Olivier Burri EPFL SV PTECH BIOP
 * for Noémie Chabot, Vastenhouw Lab
 * 
 * Last update: 01-10-2021
 * 
 * Dependencies: EasyXT https://github.com/BIOP

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// Make 3D Shell and measure intensity at given thicknesses
// By Olivier Burri, EPFL - SV - PTECH - BIOP
// As a response to an ImageSC forum post: 
// https://forum.image.sc/t/help-with-shell-analysis-of-nuclei/54342
// Last update: 2021/07/23

raw = getTitle();

close("\\Others");