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EMBL BioImage Data Analysis

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Timeline of @cmci_

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RT @ArkThul: Finally out !! A little chapter : Structure and Fluorescence Intensity Measurements in Biofilms In the book: Computer Optimize…
About 2 days, 2 hours ago by: Kota Miura (@cmci_)

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RT @BioImagingUK: @UniofOxford is recruiting a Informatics Scientist/Developer duties will include developing analysis methodologies ba…
About 2 days, 2 hours ago by: Kota Miura (@cmci_)

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RT @AJPathology: #Pathology Image Analysis Using Segmentation Deep Learning Algorithms. FREE Review in AJP's newest topic area, #MachineLea…
About 2 days, 13 hours ago by: Kota Miura (@cmci_)

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RT @iamkenneyor: IMAGING AFRICA Microscopy and Image Analysis Workshop for African Researchers There is no application or registration fee…
About 2 days, 13 hours ago by: Kota Miura (@cmci_)

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RT @leandroscholz: BIAFLOWS: A collaborative framework to benchmark bioimage analysis workflows https://t.co/RqZRffE3PS
About 3 days, 10 hours ago by: Kota Miura (@cmci_)

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RT @christlet: 🚨 LUT alert 🌈 Turbo, a new and improved rainbow LUT from @GoogleAI: https://t.co/FPaQ2zZtzE Will get it into NeuroCyto LUTs…
About 4 days, 6 hours ago by: Kota Miura (@cmci_)
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Algorithm FRAP Fiji ImageJ ImageJ Plugin ImageJ Plugin 3Dviewer Imaris Java Javascript Python R added 201904 Freiburg bias blog dokuwiki fiji google imagej java libraries matlab meetings neubias news papers python references software webadmin




CMCI weblog

Python <- (ImageJ, R)

Setup and a simple example for parallel use of ImageJ and R from Python (Jython) is documented. See Here.

R and ImageJ

R is a statistical computing package, and ImageJ is image processing and analysis software (actually, R could do image processing and ImageJ could also do statistics, but not usually used and tools are limited). Ideal work is then to somehow combine these two.

Such attempts has not been rare. Several attempts has been made. Project such as RImageJ is one of such.

http://romainfrancois.blog.free.fr/index.php?category/R-package/RImageJ

Recently, an integrated interface is available.

Bio7
http://129.70.40.49/modelling/?page_id=75

It seems that this project is mostly oriented towards ecology analysis, but the basic concept is to ease passing data between R and ImageJ. There many instructions on example usage of the software.

Java - R JRI - Java/R Interface http://www.rforge.net/JRI/

Matlab - R

very well documentation comparing Matlab and R.

http://www.math.umaine.edu/~hiebeler/comp/matlabR.html

Linked PDF contains huge number of functions in R equivalent to Matlab functions. Some useful discussions on difference between R and matlab could be found in

http://stackoverflow.com/questions/1738087/what-can-matlab-do-that-r-cannot-do

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