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EMBL BioImage Data Analysis



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RT @haesleinhuepf: Hi #BioImageAnalysis #SciTweeps, how many image and/or data analysis books do you own? 📚🙃 If you have a favorite book,…
About 7 hours, 28 mins ago by: Kota Miura (@cmci_)

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RT @ahklemm: TissUUmaps 3.1 is here! 🥳 Try it out, take a tour, join our webinar ! #bioimageanalysis #TissUUmaps Webinar:
About 7 hours, 28 mins ago by: Kota Miura (@cmci_)

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RT @TheSquishyLab: Excited to release our latest work, led by @hbozhao in collaboration with our friend Andrej Košmrlj! In this preprint…
About 3 days, 13 hours ago by: Kota Miura (@cmci_)

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Though there is a plugin solution by Niko ( ) another solution can be to add new org.scijava…
About 3 days, 17 hours ago by: Kota Miura (@cmci_)

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I mostly have used print, IJ.log, and System.out.println in my Jython script for logging but recently encountered…
About 3 days, 17 hours ago by: Kota Miura (@cmci_)

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RT @JCellBiol: Image-based pooled whole-genome #CRISPRi screening for subcellular phenotypes, developed by @gil_kanfer @youle_rj @LabYoule
About 3 days, 21 hours ago by: Kota Miura (@cmci_)

ImageJ Macro Fragments

Some notes on ImageJ macro

Getting the number of Cores

th = eval("script","Runtime.getRuntime().availableProcessors();");

Loading ROIs from a file in Internet

shell command “curl” should be available in your local machine. See here for installation.

run("Blobs (25K)");
path = getDirectory('imagej')+"";
exec("curl", "-LJO", "", "--output", path);
roiManager("Show All");

Getting Pixel Coordinates within a Polygon ROI

Roi.getContainedPoints(xps, yps); 
for(i=0; i<xps.length; i++) {
	xpos = xps[i];
	ypos = yps[i];
	pixval = getPixel(xpos, ypos);
	print("("+ xpos + ", " + ypos + ") ", pixval);

Ways of getting the file basename

filepath = "/my/path/to/great_image.tif";

//Method 1, string indexing
basename = substring(filepath, lastIndexOf(filepath, "/")+1, lastIndexOf(filepath, "."));
print("Method 1: ", basename);

//Method 2, regular expression
basename = replace(filepath, "(.*\\/)(.*)\\..{3,5}$", "$2");
print("Method 2: ", basename);
//... in this case, it's also possible to get the parent directry just with a small modification
parent = replace(filepath, "(.*\\/)(.*)\\..{3,5}$", "$1");
print(".... parent: ", parent);

//Method 3, use a specific command
//from ver. 1.52r
basename = File.getNameWithoutExtension(filepath);
print("Method 3: ", basename);
//... it's also possible to get the parent directory with a command. 
parent = File.getDirectory(filepath);
print(".... parent: ", parent);

Convert black pixels to white in RGB image

for (j =0; j<getHeight();j++){
	for (i=0; i<getWidth();i++){
		pix =  getPixel(i, j);
		sum = sumRGB(pix);
		if (sum == 0){
			setPixel(i, j, 0xffffff);

function sumRGB(RGBpixval){
	sum = getR(pix) + getG(pix) + getB(pix);
	return sum;

function getR(RGBpixval){
	rf = (RGBpixval & 0xff0000)>>16;
	return rf;       
function getG(RGBpixval){
	gf = (RGBpixval & 0x00ff00)>>8;
	return gf; 
function getB(RGBpixval){
    bf = (RGBpixval & 0x0000ff); 
    return bf;        

documents/201021ijmacrofragments.txt · Last modified: 2021/12/07 09:09 by kota