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EMBL BioImage Data Analysis



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RT @albertcardona: Estimating the number of users of an image processing tool, using various data, educated guesses from tool writers, and…
About 1 day, 19 hours ago by: Kota Miura (@cmci_)

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Proud to see a copy in the hand of the original author!
About 3 days, 5 hours ago by: Kota Miura (@cmci_)

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... in fact, the @haesleinhuepf contribution is not an image data set but a set of IJ macros.
About 3 weeks, 4 days ago by: Kota Miura (@cmci_)

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Addition of three image data to the NEUBIAS community @ ZENODO. Thanks to the contributors! @_pm_lab…
About 3 weeks, 4 days ago by: Kota Miura (@cmci_)

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RT @petebankhead: Calling all @QuPath users, we need your help! Please complete our survey to help us understand your needs & support our f…
About 3 weeks, 6 days ago by: Kota Miura (@cmci_)

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RT @JCellBiol: In this Viewpoint, @samjlord @KatrinaVelle @MullinsLab & @FritzLaylin propose a method to better display #reproducibility in…
About 1 month ago by: Kota Miura (@cmci_)
Algorithm Document FRAP Fiji ImageJ ImageJ Plugin ImageJ Plugin 3Dviewer Imaris Java Javascript Python R added 201904 Freiburg bias blog dokuwiki fiji google imagej java libraries matlab meetings neubias news papers python references software webadmin

CMCI weblog

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");

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;        

Server moved

The web server hosting this wiki has moved from EMBL to InMotion. The move was rather straight forward, but as is in the subdomain, htaccess file was tweaked around to enable to stay as it is while moving only the wiki to be redirected from to

Anycase, InMotion seems to be fast enough for rendering (even though it's in US).

Nature Physics Sept. 2013 Cover Page

The ImageJ plugin "Temporal-Color Code" was used for the analysis of the contraction of actomyosin gel and now in the cover page of Nature Physics, September 2013 issue. D. L. Taylor's “Solation-Contraction Coupling” hypothesis now on the move.

Thanks to José Alvarado for his kind acknowledgement and a big applause for his successful publication!

To be in R programming course

I do write some scripts in R but not really serious programming. As I am interested in advanced use of R, I will be in the following course organized by Wolfgang Huber.

The course seems to match with my stage, as it explains

This course is designed for users who have experience with writing R scripts, and who now want to advance one step further, into producing more durable and robust software projects and code that is usable by others.

As I always have had a plan to migrate FRAPcalc program from IgorPro to R and also add some more functionalities, this course should be the one I should attend… I thank Wolfgang for his initiative in making this course available. Besides, I am happy to see another EMBL centre being active!

BIAS 2013 wiki page

There will be “EMBL Master course on BioImage Data Analysis” in May, and I am preparing for this course with Christoph Moehl (Bonn) and Sebastien Tosi (Barcelona). For the course we want to be interactive so we now have a wiki for the course:

We abbreviate the course title “BIAS 2013”. Registration deadline is in February, and we will be waiting for many applications!

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Weblog Archive

blogtng/blogtop.txt · Last modified: 2021/01/25 02:26 by kota