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EMBL BioImage Data Analysis

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Timeline of @cmci_

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RT @biomicugm: Topics: Biostatistics, computational evolutionary biology, computational genomics and proteomics, graph models, image analys…
About 4 days, 16 hours ago by: Kota Miura (@cmci_)

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RT @JustinMCrocker: We are looking for an interdisciplinary EIPOD postdoc to join our group @EMBL! Potential projects with @Eileen_Furlong,…
About 4 days, 16 hours ago by: Kota Miura (@cmci_)

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RT @BioImagingUK: This maybe of interest to the @NEUBIAS_COST @openmicroscopy communities #imageAnalysis #imagingScientist https://t.co/I5
About 4 days, 16 hours ago by: Kota Miura (@cmci_)

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RT @BioImagingUK: Software developer position on large image data analysis - working closely with the lab of @bayraktar_lab @sangerinstitut…
About 1 week, 2 days ago by: Kota Miura (@cmci_)

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RT @AssafZaritsky: Modeling the interplay of lamellipodial motion and the intercellular actomyosin cable during epithelial wound healing h…
About 1 week, 2 days ago by: Kota Miura (@cmci_)

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RT @jytinevez: @florianjug says be careful when using #CARE for intensity based quantification; CARE restoration is like a non linear trans…
About 1 week, 4 days ago by: Kota Miura (@cmci_)
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Algorithm FRAP Fiji ImageJ ImageJ Plugin ImageJ Plugin 3Dviewer Imaris Java Javascript Python R 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)