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EMBL BioImage Data Analysis

EuBIAS

NEUBIAS

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@EntraCod @COSTprogramme @NEUBIAS_COST Yes everyone indeed. Thanks for the suggestion.
About 2 hours, 37 mins ago by: Kota Miura (@cmci_)

cmci_ avatar

RT @SimonFlyvbjerg: Fresh off Springer's open access press: "Bioimage Data Analysis Workflows" - the book! #BioImageAnalysis https://t.co
About 7 hours, 21 mins ago by: Kota Miura (@cmci_)

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@COSTprogramme @NEUBIAS_COST Thanks to the authors and editors: @perrinepgil Sébastien Tosi Julien Colombelli… https://t.co/GVlRWoqGxr
About 8 hours, 2 mins ago by: Kota Miura (@cmci_)

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Now online, "Bioimage Data Analysis Workflow". https://t.co/stW12drKaS Thanks to the support by @COSTprogramme ,… https://t.co/pgJck70nW6
About 8 hours, 9 mins ago by: Kota Miura (@cmci_)

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RT @Datascience__: Dynamic allocation of computational resources for deep learning-enabled cellular image analysis with Kubernetes https://…
About 3 days, 8 hours ago by: Kota Miura (@cmci_)

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RT @mariana_deniz: Many thanks to the @NEUBIAS_COST instructors and organizers for an exciting and stimulating course on image analysis 😁😁…
About 3 days, 13 hours 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)