We often hear retraction of papers with fake image data like gel images with hand-drawn bands and cleanups, but in addition to such elementary-level mistakes, there are image analyses used in papers that are scientifically questionable. With Simon, we tried to shed light on this overlooked problem and propose a solution.

Details of motivations, the design, and paedagogic concepts of NEUBIAS Bioimage Analysis schools, started in 2017, are now in a manuscript. I wrote the “Bioimage Analyst School” part, and am quite satisfied to have the written record of our struggle and achievements, that I did together with the bioimage analysis genius Jean-Yves Tinevez (The Pasteur Institute, Paris).

F1000R NEUBIAS Gateway: Highlights from the 2016-2020 NEUBIAS training schools for Bioimage Analysts: a success story and key asset for analysts and life scientists

The paper describing the Bleach Correction Plugin (for ImageJ) is now published.

https://f1000research.com/articles/9-1494

Please cite this paper if you are using this plugin!

Some notes on ImageJ macro

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

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

run("Blobs (25K)");
path = getDirectory('imagej')+"RoiSet.zip";
print(path)
exec("curl", "-LJO", "https://github.com/mutterer/weird/raw/master/RoiSet.zip", "--output", path);
roiManager("Open",path);
roiManager("Show All");
File.delete(path);

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);
}

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);

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;        
}	

We now have a new book "Bioimage Data Analysis Workflow"published from Springer, topics of which are centered around bioimage analysis workflows. The book is open access - thanks to the support from COST Action.

As of May 3rd 2016, supported by COST grant, NeuBIAS officially launched for creating a stronger and broader network among bioimage analysts: read "EuBIAS Manifesto (2013, DOI:10.5281/zenodo.18047)" for more details about our initial motivation. The official document stating our activities is here (PDF)

BIAS has been a small group, and EuBIAS has been a bit larger but now with NeuBIAS, it's big!

EMBL Master Course for Bioimage Data Analysis (BIAS2016): Registration is now open, deadline on April 15th.

Official Website: http://www.embl.de/bias2016

Course Wiki: BIAS2016 wiki

A new book is now online: “Bioimage Data Analysis”. The instructors of EMBL Bioimage Data Analysis coauthored 10 chapters on practical techniques for analyzing image data in biology. E-books are downloadable free of charge from the following link.

Bioimage Data Analysis (2016), Wiley-VCH

For sample image data and codes, please download from the following link:

Bioimage Data Analysis: Materials

The CMCI seminar has been either spontaneous or took a form of mini-symposium, but now in a new format.

Every three weeks, seminar member gathers and two of them present image analysis problems / solutions or reads a paper. For more details and the schedule, see this page.

The 2nd “EMBL Master course on BioImage Data Analysis” will be in May. I , Sebastien Tosi (Barcelona) and Perrine Paul-Gilloteaux will be organizing the course. Here is the wiki page for this year.

http://cmci.embl.de/shared/bias2014

I added biography of invited speakers, so please check if you are interested! By the way, we abbreviate the course title as “BIAS2014”.