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EMBL BioImage Data Analysis

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Timeline of @cmci_

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Impressive and swift moderation @helenajambor !
About 3 hours, 33 mins ago by: Kota Miura (@cmci_)

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RT @LuisDVerde: Now available as a #ggplot2 geom thanks to @naupakaz https://t.co/zOaMWvzd8k https://t.co/AXYBCeGyw6
About 3 hours, 36 mins ago by: Kota Miura (@cmci_)

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RT @helenajambor: awesome, within 2 days .@naupakaz made a code publicly available for anyone wanting to make the half-and-half-plot FYI @…
About 3 hours, 37 mins ago by: Kota Miura (@cmci_)

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RT @dgaboriau: Thread on data visualisation: ggplots, boxplots and violin plots https://t.co/QZE7xQtaa3
About 9 hours, 14 mins ago by: Kota Miura (@cmci_)

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RT @christlet: SUSHI from Valentin Nāgerl lab allows super-resolution microscopy of neuronal morphology by STED imaging of extracellular sp…
About 12 hours, 25 mins ago by: Kota Miura (@cmci_)

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RT @christlet: Our work with @HenriquesLab and @MercerLab on SQUIRREL highlighted on the @CNRS website (in French, and we even found a pun!…
About 12 hours, 26 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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Weblog Archive

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