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EMBL BioImage Data Analysis

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Timeline of @cmci_

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Anna getting ready for her talk @NEUBIAS_COST workshop starting in 3 min. https://t.co/Dl9ZI0NKDs
About 6 hours, 14 mins ago by: Kota Miura (@cmci_)

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RT @MIAP_Freiburg: @MIAP_Freiburg @UniFreiburg will host another basic Fiji @FijiSc/#ImageJ workshop on November 14th-15th 2018 with Kota M…
About 6 hours, 15 mins ago by: Kota Miura (@cmci_)

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RT @haesleinhuepf: Let's measure with @laure_plantard and #ImageJ at #NEUBIAS #TS8 🤘 https://t.co/oVpyDWP3HT
About 1 day ago by: Kota Miura (@cmci_)

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RT @haesleinhuepf: Tracking cells on steroids: @jytinevez introducing #Mamut just next door #NEUBIAS #TS9 https://t.co/cKYq55i2JU
About 1 day ago by: Kota Miura (@cmci_)

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RT @haesleinhuepf: Anna Klemm from @scilifelab lifting us to the next level: tracking objects #NEUBIAS #TS8 https://t.co/FSkyLXilAO
About 1 day ago by: Kota Miura (@cmci_)

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RT @dn_mason: Check out our latest @biorxivpreprint (/w @Rosalierrr @ViolaineSee, @raphavisses & Rachel Bearon)! A workflow for imaging, tr…
About 1 day, 2 hours ago by: Kota Miura (@cmci_)
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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
		seg.loadTrainingData(fullpath);
		//"Train classifier" button
		try{
			seg.trainClassifier();
		}catch(Exception e){
			e.printStackTrace();
		}
		//"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”) (http://pacific.mpi-cbg.de). 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

Hackathon:

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

Talks:

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 (elisabeth.hillier@embl.de )


For more updates on info, check http://cmci.embl.de.

We are looking forward to hearing from you.

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

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blogtng/blogtop.txt · Last modified: 2016/05/24 05:46 (external edit)