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Image Processing and Analysis @EMBL

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EMBL BioImage Data Analysis 2013 EMBL BioImage Data Analysis 2014 EMBL BioImage Data Analysis 2015

EuBIAS2013, Barcelona EuBIAS2014/15, Paris

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Timeline of @cmci_

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RT @sebastianmunck: Measure everything and ask questions later. Great talk by Anne Carpenter #ELMI2015
About 2 days, 2 hours ago by: Kota Miura (@cmci_)

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RT @manel_bosch: The end of the conference diner in #elmi2015 @cmci_ and the organizers on the table. Great job to all of them.
About 2 days, 2 hours ago by: Kota Miura (@cmci_)

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#ELMI2015 model organism session: the last speaker of this ELMI, @PavelTomancak on stage. after Planaria, Parhyale, now fly.
About 2 days, 2 hours ago by: Kota Miura (@cmci_)

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#elmi2015 Rémi Galland presenting amazing cell culture wells (chip), equipped with mirrors for SPIM.
About 3 days, 5 hours ago by: Kota Miura (@cmci_)

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@ManuelTHERY thanks, I think you could say "cell size maintenance seems to be an active process, not passive, consuming a lot of energy".
About 4 days ago by: Kota Miura (@cmci_)

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"Physical planning and construction of a microscope facility @ Copenhagen" by Clara Prats #ELMI
About 5 days, 9 hours ago by: Kota Miura (@cmci_)


Centre for Molecular and Cellular Imaging

CMCI@EMBL drives image analysis / processing activity by power of human networking.
Please feel free to comment on any page.


Triweekly CMCI image analysis seminar launched

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.

BIAS 2014 wiki 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.

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

EuBIAS 2013, Successful!

 EuBIAS 2013, Barcelona The European Bioimage Analsis Symposium (EuBIAS) 2013 ended successfully! The meeting was with many active discussions, the course impressed students, the taggathon (we invented this event) generated a new type of bioimage analysis tool aggregator Great developers, great analysts, great users! Community, community, community!

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!


For strengthening the bioimage analysis community, we organize the first EuBIAS meeting in Barcelona. For those of you with problems such as:

  • Which tool is appropriate for my question?
  • Who should I ask my very specific question about image analysis?
  • I want to increase my skill, but I do not know how.
  • I am a developer and want to know more demands of biologists.
  • I became an image analysts specialist. Is there a community for me?

Join the meeting and get to know top-developers, leading image analysts and biologist with similar problems!

More details and registration:

The 3rd CMCI symposium, July 5th, 2013

We will have the third CMCI image analysis symposium on July 5th (Fri), 2013. See more details.

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!

New Server

This site has migrated to a new server and also now running with the most recent Dokuwiki! You might not recognize this move and upgrade, but this could not have been done with helps and hackings by Agustin Villalba @ IT service. This Dokiwiki web application is running with sqlite3 (Dokuwiki does not deal with sqlite3 normally). Thanks to Agustin!

Two Lectures on Classification and Clustering, April and May

Coupled lectures on Classification and Clustering will be given in the CMCI seminar in April and May. These two approaches have been widely used for screening and system descriptions, but there seems to be more in the future in terms of image processing and analysis, as we have seen in the CMCI seminar in March. For this reason we asked for introduction for these two topics by two experts in the EMBL. Bernd Fischer will give us a lecture on Classification and Machine learning, and Jean-Karim Heriche will give a lecture on cluster analysis.

CMCI seminar, Jan 27, 2012 (Fri) 15:00- @room 518 (Building 13)

Kota will talk about cell tracking in Drosophila embryo and Andrea Picco will talk about his work on subpixel resolution tracking of yeast endocytosis.


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