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EMBL BioImage Data Analysis



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RT @SimonFlyvbjerg: Image analysis job opening in Wonderful Copenhagen
About 11 hours, 1 min ago by: Kota Miura (@cmci_)

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RT @JekelyLab: Interested in connectomics? Join us in stunning Exeter! Postdoc opening to work on Platynereis serial EM data @UoE_Jobs @Uni…
About 11 hours, 1 min ago by: Kota Miura (@cmci_)

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I like this kind of analysis - protein and organelle distributions
About 11 hours, 4 mins ago by: Kota Miura (@cmci_)

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Measuring radial intensity profile using custom IJ macro. Fig4b.
About 11 hours, 5 mins ago by: Kota Miura (@cmci_)

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RT @SfPRocur: One hashtag to follow for this kind of #sciart is #cellfie - different kinds of cells usually captured in a microscope. Look…
About 22 hours, 36 mins ago by: Kota Miura (@cmci_)

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RT @herrsaalfeld: Oh---look what just came out: @funkstille @srinituraga @cremi_challenge
About 23 hours, 55 mins ago by: Kota Miura (@cmci_)
Algorithm FRAP Fiji ImageJ ImageJ Plugin ImageJ Plugin 3Dviewer Imaris Java Javascript Python R bias blog dokuwiki fiji google imagej java libraries matlab meetings neubias news papers python references software webadmin

CMCI weblog

Trainable Segmentation

A new Fiji plugin called "Trainable Segmentation" was created during the Fiji Hackathon and also further upgraded since last March, by the effort of Verena Kaynig, Ignacio Arganda-Carreras and Albert Cardona. This is quite handy if you want to train computer to let it do segmentation automatically, as it is possible to save trained data and re-use it.

Ignacio modified the code so that it could be accessed as library. Here is a sample methods of accessing the plugin from another plugin. Path to the data is set in the first method, and the second method receives ImagePlus instance (image or stack) as argument and outputs segmented image/stack.

	private static String fullpathdata = "ttt";

	public static void setDatapath(String fullpath){
		fullpathdata = fullpath;
		IJ.log("Loading data from " + fullpathdata + "...");

	public static ImagePlus core(ImagePlus imp){

		ImageStack stack = imp.getStack();

		ImagePlus imptemp = new ImagePlus("training slice", new ByteProcessor(imp.getWidth(), imp.getHeight()));
		ImageProcessor ipc = imptemp.getProcessor();// = imp.getProcessor().duplicate();		
		String fullpath;
		fullpath = fullpathdata;

		ipc = stack.getProcessor(1).duplicate();
		//using Ignacio's update
		Trainable_Segmentation seg = new Trainable_Segmentation(new ImagePlus("temp", ipc));
		//"Load Data" button
		//"Train classifier" button
		}catch(Exception e){
		//"Apply Classifier" button
		ImagePlus binimp = seg.applyClassifierToTestImage(imp);
		return binimp;

FIJI/ImageJ Hackathon / March 15th-26th, 2010 @EMBL

for details, go to FIJI 2010 Page

Dear All,

We would like to draw your attention on the following initiative:

Fiji/ImageJ Hackathon
March 15th-26th, 2010
Room 6.51a

A group of around 15 core developers of FIJI/ImageJ will meet here at the EMBL with the aim of enhancing 3D visualization and timelapse analysis in ImageJ/Fiji.

What is Fiji?

Fiji (“Fiji is just ImageJ”) ( It emerged as a user-driven response to organize ImageJ's collection of plugins, along with comprehensive user documentation, and version-controlled code for developers. The developers introduced new ImageJ libraries for image registration, stitching, segmentation, feature extraction, 3D visualization, and numerous others.

What is an Hackathon?

It is a software development sprints. Hosting such an initiative here at the EMBL is a great opportunity for both EMBL imaging processing specialists and researchers to contribute to the open Fiji project, and have a saying in the development of this widely popular software.

Summary of the initiative


Please note that the Hachathon is an open platform however, if you want to participate please send and email to Kota Miura ( ).


17/3 (Wed) 11am @Small Operon
Erwin Frise
“Exploring spatial gene expression during early development of Drosophila”

19/3 (Fri) 11am @Small Operon
Pavel Tomancak
“New tricks for comparative genomics analysis of gene expression regulation in Drosophila”

24/3 (Wed) 4pm @Small Operon
Mark Longair
“Neuron Tracing and Computational Neuroanatomy with Free Software”

Hands-on tutorials:

17/3 (Wed, 2:30pm-5:00pm in Room 202): Image segmentation workshop
18/3 (Thu, 2:30pm-5:00pm in Room 202): Image registration workshop

If you would like to participate in these tutorials, send an email to Elisabeth Hillier ( )

For more updates on info, check

We are looking forward to hearing from you.

Best wishes,
Kota Miura (CMCI) and Francesca Peri (DB)

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