measure_multiImage_CZI_5chMP.ijm

macro 'convert CZI to tiff' {

/*
 * - converts czi files into TIFF and analyses them. 
 * - the macro ask for an input folder that should contain 1 or more czi files.
 * - if they are tilescans, it saves each tile out as a tif and analyses independently.
 * - each series is saved as one tiff. The name of the series is appended to the file name.
 * - The TIFFs are saved in a folder generated by the macro in the same 
 * - parent folder as the lifs, with the same prefix for the folder name, with TIFF suffix.
 * - The analyses are stored in separate folders in a similar manner with the names _Areas
 * - and _Objects
 * 
 */

run("Bio-Formats Macro Extensions");


dir1 = getDirectory("Choose folder with czi files ");
list = getFileList(dir1);

setBatchMode(true);

// create folders for the tifs
	dir1parent = File.getParent(dir1);
	dir1name = File.getName(dir1);
	dir2 = dir1parent+File.separator+dir1name+"_Tiffs";
	dir3 = dir2+File.separator+"_Areas";
	dir4 = dir2+File.separator+"_Objects";
	if (File.exists(dir2)==false) {
				File.makeDirectory(dir2); // new directory for tiff
		}
	if (File.exists(dir3)==false) {
				File.makeDirectory(dir3); // new directory for area analsysis
		}
	if (File.exists(dir4)==false) {
				File.makeDirectory(dir4); // new directory for object analysis
		}
 
for (i=0; i<list.length; i++) {
	showProgress(i+1, list.length);
	print("processing ... "+i+1+"/"+list.length+"\n         "+list[i]);
	filename = dir1 + list[i];
		if (endsWith(filename, "czi")){
		path=dir1+list[i];

	//how many series in this czi file?
		Ext.setId(path);//-- Initializes the given path (filename).
		Ext.getSeriesCount(seriesCount); //-- Gets the number of image series in the active dataset.
	
		for (j=1; j<=seriesCount; j++) {
		
		run("Bio-Formats", "open=path autoscale color_mode=Default view=Hyperstack stack_order=XYCZT series_"+j);
	
		name=File.nameWithoutExtension;
		seriesname=name;
	//	saveAs("/Users/glyn_nelson/Desktop/test/cziTest/heart_point3airy_decon_with_measured_PSF-2.tif");
		saveAs("TIFF", dir2+File.separator+name+"#"+j+".tif");

//Now analyse the image
//modified for 4 channel images ch1 920 SHG, ch2 920 GFP, ch3 1040 SHG, ch4 1040 AF/vasc dye
title =getTitle();
rename("tilescan1cleaner_4wk");
run("Make Composite");

//first merge both shg as a minimum to remove shot noise
run("Duplicate...", "title=shg1 duplicate channels=1");
selectWindow("tilescan1cleaner_4wk") ;
run("Duplicate...", "title=shg2 duplicate channels=4");

imageCalculator("Min create", "shg1","shg2");
selectWindow("Result of shg1");
rename("SHG_" + title);
run("Despeckle");
run("Set Measurements...", "area mean standard perimeter integrated area_fraction limit display redirect=None decimal=3");
run("Measure");
close();
selectWindow("shg1");
close();
selectWindow("shg2");
close();

//now clean up GFP using the AF in red channel
selectWindow("tilescan1cleaner_4wk") ;
run("Duplicate...", "title=green duplicate channels=2");
//selectWindow("tilescan1cleaner_4wk") ;
//run("Duplicate...", "title=greenBgrnd duplicate channels=3");
//imageCalculator("Subtract create", "green","greenBgrnd");
//selectWindow("Result of green");

//setAutoThreshold("Huang dark");
//run("Convert to Mask");
//run("Close");
rename("GFP_" + title);
//setMinAndMax(1000, 4095);
//run("Despeckle");
//run("Apply LUT");
run("Measure");
//rename("binary");
saveAs("Results", dir3+File.separator+name+"#"+j+"_GFPandColl_Area.csv");
run("Clear Results");

selectWindow("GFP_"+title);

//setAutoThreshold("IsoData dark");

//setAutoThreshold("Huang dark");
//run("Convert to Mask"); //needs to be made binary for the dilate to run
//run("Dilate");
run("Gaussian Blur...", "sigma=4"); //obviously loses the binary-ness
//setAutoThreshold("MaxEntropy dark");
run("Convert to Mask");
//run("Make Binary");
//selectWindow("binary");
rename("GFPbinary_" + title);
run("Analyze Particles...", "size=30.00-Infinity display");
//run("Analyze Particles...", "size=30-Infinity summarize");
//SelectWindow(Summary);
saveAs("Results", dir4+File.separator+name+"#"+j+"_GFP_Objects.csv");
run("Clear Results");



		run("Close All");
//		run("Collect Garbage");
		
	}

}
//showMessage(" Well, I think we gave them a damn good thrashing there, what what??");	
run("Close All");
setBatchMode(false);

}
showMessage(" Well, I think we gave them a damn good thrashing there, what what??");	
 // macro