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EMBL BioImage Data Analysis

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Timeline of @cmci_

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Yoshikatsu Sato, the head of microscope facility @NagoyaITbM presenting practicals #EMBOLivePlant https://t.co/SVrkfOKQCn
About 18 hours, 42 mins ago by: Kota Miura (@cmci_)

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Miyo Terao Morita showing analysis of gravitropism using centrifuge microscope they newly developed. I only know… https://t.co/Atj9E4QJAY
About 19 hours, 14 mins ago by: Kota Miura (@cmci_)

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@KeikoUTorii ... which then became the cover page of Development cell. convincing. https://t.co/XBgiqJpHog
About 20 hours, 12 mins ago by: Kota Miura (@cmci_)

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@KeikoUTorii model-based hypothesis lead to experiment results with single guard cell development or multiple >2 gu… https://t.co/oGhh4NJMPh
About 20 hours, 19 mins ago by: Kota Miura (@cmci_)

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now, @KeikoUTorii on stomata development - how very specific cell fate decisions are made, with proper spacing bet… https://t.co/XoR8tpB5WR
About 20 hours, 36 mins ago by: Kota Miura (@cmci_)

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@YvonJaillais talk on nanoclustering of ROP6, great analyses using various approaches to assess protein mobility… https://t.co/WHrzBsWTYJ
About 20 hours, 52 mins ago by: Kota Miura (@cmci_)
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CMCI weblog

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 (http://bigwww.epfl.ch/eurobioimaging/). 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.

Python IP cookbook on the way

Started to write Python Image Processing Cookbook.

http://cmci.embl.de/documents/110816pyip_cooking

It's a bit surprising that there is not much information about Python Image Processing, considering it's potential. Most of the tutorial pages are about PIL module which only allows you to deal with 8-bit images.

I have been comparing Python IP and Java IP, and think that these two worlds could be complement to each other. Java is much stronger with Image Processing libraries but weak with statistics and numerical treatments. For the latters, Python is much more efficient. Python is also better for plotting graphs in 2D and 3D.

Drop Script Plugin for ImageJ

Drop Script Plugin for ImageJ is now available for download.

Server ImageJ Launcher

For easy access to use EMBL cluster for calculation using ImageJ, I tested using Jsch, a pure SSH2 implementation in Java (http://www.jcraft.com/jsch).

I made a ImageJ launcher that runs server-side ImageJ on local desktop (see GitHub repository ServerIJ). X should be ready for hosting the GUI. For further development, interface will be more boring as only some fields to input name of shell script and some options (path name to image files, macro or scripts) will be what you will see.

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