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EMBL BioImage Data Analysis



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@MarionLouveaux I can't find Astha's twitter account, but she is here already in twitter. She's got the poster priz…
About 1 hour, 25 mins ago by: Kota Miura (@cmci_)

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one of the discussion topics with @MarionLouveaux and Astha was "how to deal with people asking 'I want to find dif…
About 1 hour, 26 mins ago by: Kota Miura (@cmci_)

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Ah wrongly mentioned. @ilastik_team
About 2 hours, 53 mins ago by: Kota Miura (@cmci_)

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... a pic kindly taken by Fred Hamprecht who just by chance passed by. Thanks Fred! @ilastik
About 2 hours, 56 mins ago by: Kota Miura (@cmci_)

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RT @Biosdfp: Amazing metal-replica electron microscopy of cortical actin in membrane blebs from the Svitkina and Alexandrova labs in latest…
About 21 hours, 52 mins ago by: Kota Miura (@cmci_)

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RT @PLOSBiology: EmbryoPhenomics - an #OpenSource platform for high-throughput #phenome screening of aquatic #embryos. Proof-of-principle c…
About 21 hours, 53 mins ago by: Kota Miura (@cmci_)
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CMCI weblog

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!

Latex to Dokuwiki

I have been searching for a convinient way to convert Latex to Dokuwiki (also MSword doc to dowuwiki as well).

Never been really successful, though there are some Dokuwiki pluings that converts Dokuwiki to Latex and vice versa. Problem of the plugin is that latex should be installed in the webserver, but that is not the case in the EMBL. and I cannot install them as I am not the administrator.

One way I figured out by now is the following detour.

  1. Convert Latex document to Markdown using Pandoc.
  2. Use markdown plugin (of Dokuwiki). Just copy and paste the markedown text in the dowkuwiki, and bound that part with <markdown> tag

Discovering the markdown plugin was a big change for this purpose. Not only latex docs, but MS doc and docx could be converted using the Pandoc and be pasted into Dokuwiki.

... so I wrote this short report using the markdown syntax. The plugin actually uses markdown extra, an enhanced version.

ISBI 2012, Satellite Meeting

A picture with the ImageJ founder, Wayne Rusband.

A meeting titled “Bioimage analysis software: is there a future beyond ImageJ?” took place in Barcelona between April 31st and May 1st ( Some key presentations were given by Wayne Rusband, Johannes Schindlin, Curtis Rueden and all the famous developers among ImageJ community and more software such as Icy and BioimageXD.

Wayne talked about how he started developing NIH Image in 1987, with some pictures of initial Apple II machine he was developing with. The software was coded in pascal, and I told him that I started using it in 1993 and was fascinated by the ImageJ macro language. He also informed us with his latest update, pixel inspector that shows the distribution of values in the vicinity of the cursor location.

Intensive discussions on strengthening the community was held as well, mainly in the direction of setting up a core portal and planning periodic meetings.

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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