Useful_FIJI_code/Batch_Z-stack_Trimmer.ijm at master · NickCondon/Useful_FIJI_code · GitHub

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print("\\Clear");

//	This script has been made with the help of Nicholas Condon's script Generator

//	MIT License
//	Copyright (c) 2025 Nicholas Condon , n.condon@uq.edu.au
//	Permission is hereby granted, free of charge, to any person obtaining a copy
//	of this software and associated documentation files (the "Software"), to deal
//	in the Software without restriction, including without limitation the rights
//	to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
//	copies of the Software, and to permit persons to whom the Software is
//	furnished to do so, subject to the following conditions:
//	The above copyright notice and this permission notice shall be included in all
//	copies or substantial portions of the Software.
//	THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
//	IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
//	FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
//	AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
//	LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
//	OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
//	SOFTWARE.
scripttitle= "DRAFT Manasa Script 2";
version= "0.4";
date= "23-10-2025";
description= "Cell, Puncta & Donut Measurer";

/*
 * v0.3
 * 	Added mito raw integrated density measurements
 * 	changed NLRP mean to integrated density measurements
 *
 * v0.4
 * Changed from intden to rawintden
 *
 */


showMessage("ImageJ Script Information Box", "<html>
    +"<h1><font color=black>ImageJ Script Macro: "+scripttitle+"</h1>
    +"<p1>Version: "+version+" ("+date+")</p1>"
    +"<H2><font size=3>Created by Nicholas Condon</H2>"
    +"<p1><font size=2> contact n.condon@uq.edu.au \n </p1>"
    +"<P4><font size=2> Available for use/modification/sharing under the "+"<p4><a href=https://opensource.org/licenses/MIT/>MIT License</a><h4> </P4>"
    +"<h3>   <h3>"
    +"<p1><font size=3  i>"+description+"</p1>
    +"<h1><font size=2> </h1>"
	   +"<h0><font size=5> </h0>"
    +"");
print("");
print("FIJI Macro: "+scripttitle);
print("Version: "+version+" Version Date: "+date);
print("By Nicholas Condon (2025) n.condon@uq.edu.au");
print("");
getDateAndTime(year, month, week, day, hour, min, sec, msec);
print("Script Run Date: "+day+"/"+(month+1)+"/"+year+"  Time: " +hour+":"+min+":"+sec);
print("");

// --- Parameters ---
pixelSize = 0.0353646;     // µm per pixel
radius_um = 2.0;           // circle radius in µm
radius_px = radius_um / pixelSize;


//Directory Warning and Instruction panel
Dialog.create("Choosing your working directory.");
 	Dialog.addMessage("Use the next window to navigate to the directory of your images.");
  	Dialog.addMessage("(Note a sub-directory will be made within this folder for output files) ");
  	Dialog.addMessage("Take note of your file extension (eg .tif, .czi)");
Dialog.show();

//Directory Location
path = getDirectory("Choose Source Directory ");
list = getFileList(path);
getDateAndTime(year, month, week, day, hour, min, sec, msec);

ext = ".tif";
Dialog.create("Settings");
Dialog.addString("File Extension: ", ext);
Dialog.addMessage("(For example .czi  .lsm  .nd2  .lif  .ims)");
Dialog.addNumber("What Size band would you like?", 20);
Dialog.show();
ext = Dialog.getString();


start = getTime();

//Creates Directory for output images/logs/results table
resultsDir = path+"_Results_"+"_"+year+"-"+(month+1)+"-"+day+"_at_"+hour+"."+min+"/";
File.makeDirectory(resultsDir);
print("Working Directory Location: "+path);


for (z=0; z<list.length; z++) {
if (endsWith(list[z],ext)){

	//	run("Bio-Formats Importer", "open=["+path+list[z]+"] autoscale color_mode=Default rois_import=[ROI manager] view=Hyperstack stack_order=XYCZT");
run("Bio-Formats Importer", " open=["+path+list[z]+"] autoscale color_mode=Default rois_import=[ROI manager] specify_range view=Hyperstack stack_order=XYCZT z_begin=190 z_end=260 z_step=1");

	windowtitle = getTitle();

		save(resultsDir+windowtitle);close();
}}
//exit message to notify user that the script has finished.
title = "Batch Completed";
msg = "Put down that coffee! Your analysis is finished";
waitForUser(title, msg);