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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 17 hours, 41 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 18 hours, 13 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 19 hours, 10 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 19 hours, 17 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 19 hours, 35 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 19 hours, 51 mins ago by: Kota Miura (@cmci_)
blogtng:blogtop
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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Weblog Archive

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