Image analysis in R

Question

I would like to know how I would go about performing image analysis in R. My goal is to convert images into matrices (pixel-wise information), extract/quantify color, estimate the presence of shapes and compare images based on such metrics/patterns.

I am aware of relevant packages available in Python (suggestions relevant to Python are also welcome), but I am looking to accomplish these tasks in R.

Thank you for your feedback.

-Harsh

score 9 · Answer 1 · answered Oct 17 '10 at 20:43

9

I'd start with EBImage - check out the vignette which demonstrates many of the tasks you mention.

answered Oct 17 '10 at 20:43

hadley

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Thanks hadley. I was just looking at it. It certainly seems helpful. – harshsinghal Oct 17 '10 at 20:46
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It seems like `EBImage` is not available for latest versions of R. – ffriend Jan 26 '12 at 22:44
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@ffriend `source("http://bioconductor.org/biocLite.R")`; `biocLite("BiocUpgrade")`; `biocLite("EBImage")`; – Zach Dec 19 '12 at 22:54

Janvb · Accepted Answer · 2010-10-18T09:15:31.280

Also check out the RASTER package on the R-Forge website:

http://r-forge.r-project.org/projects/raster/

It is not released to CRAN yet but it is an excellent package to import, analyse, extract, subset images and convert them to matrices). Spatial analysis is also possible.

You can download the package in R via:

install.packages("raster",repos="http://r-forge.r-project.org")
require(raster)

An example for R:

#from file
r <- raster(system.file("external/test.grd", package="raster"))
logo <- raster(system.file("external/rlogo.grd", package="raster"), values=TRUE) 
plot(logo)

Check out

?raster # and go to index of the package for an overview of all the options for image analysis.

Thanks Jan. Will surely give this a shot. Looking forward to the example. — harshsinghal, Oct 17 '10 at 20:50

score 1 · Answer 3 · answered Oct 17 '10 at 20:16

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I believe the CRAN Task View on Medical Imaging should have something for you.

answered Oct 17 '10 at 20:16

Dirk Eddelbuettel

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Thanks Dirk. I did look at the CRAN Task View, but was interested in knowing if there is more info/suggestions out there. – harshsinghal Oct 17 '10 at 20:35
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Next time please make it more clear what you have considered and what you haven't -- in order to make the questions a tad more more focused. – Dirk Eddelbuettel Oct 17 '10 at 22:30

score 1 · Answer 4 · answered Oct 17 '10 at 21:20

1

You may also be interested in Rpy which allows you to call R functions and use R packages from Python. This may allow you to have your cake (Python's imaging libraries) and eat it too (R's statistical analysis capabilities).

answered Oct 17 '10 at 21:20

Sharpie

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score 1 · Answer 5 · answered Oct 19 '10 at 02:36

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Try the rgdal package. You will be able to read (import) and write (export) GeoTiff image files from/to R.

Marcio Pupin Mello

answered Oct 19 '10 at 02:36

Marcio Pupin Mello

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Image analysis in R

5 Answers5

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