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EMBL BioImage Data Analysis

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Timeline of @cmci_

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RT @Fr_BioImaging: #onlinetraining on "Image Processing for Correlated and Multimodal Imaging Techniques" organized by @COMULIS_COST Regist…
About 7 hours, 54 mins ago by: Kota Miura (@cmci_)

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RT @jytinevez: New preprinton combining #TrackMate and #StarDist in the #ZeroCostDL4Mic framework. Work led by Guillaume and excellent col…
About 7 hours, 58 mins ago by: Kota Miura (@cmci_)

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RT @LauLauThom: Just updated the Roi 1-click tools with a cool feature 🥳 Keep the left-click maintained to preview the roi and adjust its p…
About 2 days, 14 hours ago by: Kota Miura (@cmci_)

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@KuglerElisabeth @martinjones78 @dgaboriau @WilsonAdams_ @focalplane_jcs @AcademicChatter @NEUBIAS_COSThttps://t.co/V7G5Ibfe28
About 3 days, 2 hours ago by: Kota Miura (@cmci_)

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RT @KuglerElisabeth: How can #developers help wet lab #scientists to use their analysis approaches? What's your thoughts? Interesting que…
About 3 days, 2 hours ago by: Kota Miura (@cmci_)

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RT @paqio: Exciting new all-optical data, fresh off a new prototype! Showing off beautiful holographic optogenetic activation of the cir…
About 4 days, 11 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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Weblog Archive

blogtng/blogtop.txt · Last modified: 2016/05/24 12:46 (external edit)