similar to: Image processing and analysis with R

Hi, I am looking for a R package which is capable to process and analysis pictures of tissues (stained) in an automatic way. I had a look on biops and EBImage (Bioconductor) but they are not automatic... Did you already use/know a such package ? Thanks, - Martial _________________________________________________________________ Tchattez en direct en en vidéo avec vos amis !

version.string R version 2.15.2 (2012-10-26) I am trying to install biOps on MacOS X 10.8.2 First, I have tiff, fftw-3, jpeg and set paths like cd /usr/include sudo ln -s /usr/local/include/fftw3.h for x in /usr/local/include/j*.h; do sudo ln -s $x; done for x in /usr/local/include/tiff*.h; do sudo ln -s $x; done cd /usr/lib for x in /usr/local/lib/libfftw3.*; do sudo ln -s $x; done for x in

Hi, I installed biOps on my XP, and installed the required dll packages, jpeg62.dll, libfftw3-3.dll, and libtiff3.dll, as suggested by this forum. Then it worked perfectly for about one week till this afternoon. When I tried to load biOps again, I got the following error message again Error in inDL(x, as.logical(local), as.logical(now), ...) : unable to load shared library

I have tried several times to load biOps package after reading the posts in this archive regarding the necessity of placing these two libs in the PATH (libjpeg62.dll and libtiff3.dll). I have tried locating the libs in several directories that should have worked, but I still get the following message. ------------------ Error in inDL(x, as.logical(local), as.logical(now), ...) :

Hi, I've been looking for Image Processing packages. Thresholding, Edge Filters, Dct, Segmentation, Restoration. I'm aware, that Octave, Matlab etc. would be a good address but then I'm missing the "statistical power" of R. Does anybody know of packages, projects etc. Comments on wether the use of R for such matters is useful are welcome. Greetings Thomas Kaliwe

I installed the (binary) biOps package, which can use libtiff and libfftw. Then I used macports to install the libraries (in /opt/local/lib). But I restart R and biOps still does not see the libraries. I've tried adding symbolic links from /opt/local/lib to /usr/local/lib, I've added /opt/local/lib to LIBRARY_PATH, LD_LIBRARY_PATH, and DYLD_LIBRARY_PATH, and it doesn't work. Do you

I'm running R 2.6.1 on a WXP machine. When I do the following I get an error message. > library(biOps) Error in dyn.load(file, ...) : unable to load shared library 'C:/PROGRA~1/R/R-26~1.1/library/biOps/libs/biOps.dll': LoadLibrary failure: The specified module could not be found. Error: package/namespace load failed for 'biOps' Please help, or comments about what

All, the MacOSX binary build of the biOps package is broken on cran, so I am trying to compile from source. I am very close; the trick is apparently that this package depends on fftw3, libjpeg and libtiff. My fftw3 is in /usr/local/, but my libjpeg and libtiff are in /opt/local/ since i got them through macports. In general, I'd like to keep as many of my third-party libraries as I can in the

Hello, I'm running R with windows. Could anybody help me how to install the package biOps (http://cran.mirroring.de/src/contrib/Descriptions/biOps.html) ? I cannot find it at any mirror provided by the GUI; I just found it as "tar.gz" which cannot be installed with the installation method... Maybe, I simply do something wrong? Thanks for any hint! Antje

Buenas dias a tod@s, Quisiera saber si alguien tiene experiencia con el procesamiento de imágenes (en formatos JPEG o PNG) en R y la búsqueda de similitudes / diferencias entre ellas. La idea de lo que me gustaría hacer es: tomar una imagen, cargarla en R y luego analizar su estructura. Para las dos primeras tareas, la libreria ReadImages en CRAN me ha sido útil, pero para la segunda, hasta

What software exists for digitizing video to quantify the motion of specific features in the image? I might be willing to use something that's NOT in R, though I'd prefer something in R (or at least with an R intereface). Thanks, Spencer Graves

Hi all, Am I using the correct syntax to set a custom R_LIBS when running R CMD INSTALL from the command line? I get: R_LIBS=/Users/hadley/R-dev R CMD INSTALL aL3xa-rapport-08e68ca/ # Desktop : R_LIBS=/Users/hadley/R-dev R CMD INSTALL aL3xa-rapport-08e68ca/ # * installing to library ?/Users/hadley/R? # ERROR: dependency ?ascii? is not available for package ?rapport? But: ls

I am not sure if I should ask this question in this list. But I'll try. Currently I am trying to analyze images using EBImage and biOps. One of the features that I need to extract from various images is the color spectrum, namely, which colors each image consists of. So, each image hopefully can be converted into some sort of color histogram so that color ingredients are easily comparable

Hi, I installed biOps on my XP, and installed the required dll packages, jpeg62.dll, libfftw3-3.dll, and libtiff3.dll, as suggested. Then it worked perfectly for about one week till this afternoon. When I tried to load biOps again, I got the following error message again Error in inDL(x, as.logical(local), as.logical(now), ...) : unable to load shared library

I am out of my league with this question. The following code starts the java imaging program ImageJ from within R, and displays an image (assuming ImageJ is installed on your computer). library(RImageJ) img <- IJ$openImage( file.choose() ) #pick an available .tif file img$show() # make the image object visible # An image is now displayed # find out about the objects involved >

Hello, Any advice or pointers for implementing Sobel's test for mediation in 2-level model setting? For fitting the hierarchical models, I am using "lme4" but could also revert to "nlme" since it is a relatively simple varying intercept model and they yield identical estimates. I apologize for this is an R question with an embedded statistical question. I noticed that a

Dear All, I found this nice example of PCA application on the web http://www.r-bloggers.com/principal-components-and-image-reconstruction/ and wanted to reproduce the results for myself. I installed biOps the usual way and got the message *package 'biOps' successfully unpacked and MD5 sums checked* but when loading the package, I get *Error in inDL(x, as.logical(local),

Hello everyone, I want make a variable selection  from a dataframe, but when I build this new object (using cbind) the new table (which is a matrix) I lost all the original factor names in the variables. I get 1,2,3.... Someone would be so kind and tell me if there's is a ny way to get variables in a dataframe, but not changing these factor to numbers? Thank you all. José [[alternative

Dear R list members I would be grateful if anyone could guide me to a solution for fixing my rimage package problem described below. I recently upgraded my machine from fedora core 3 to fedora core 6 and then upgraded R from version 2.3.1 from version 2.4.1. I then fired up R, tried to load the rimage library and received the following messages: > library(rimage) Error in dyn.load(x,

Hi, I'm trying to install rimage on a Mac OS X 10.4 machine. I followed the advice in previous R-help threads and got over the hurdles of having the header files in the right places, among other things. But I can't figure out what to do with this error. ice.pnl.gov:/home/waichler<949>system_profiler -detailLevel mini SPSoftwareDataType Software: System Software Overview: