Dear all, At our department we have experienced some difficulties with our microarray scanner. I am looking for some software that can read in the raw TIFF files that come out of our scanner to asses how blurry the picture is (i.e. how sharp the edges are in the picture). I would also like to know which areas of the picture are the most blurry (we suspect a left to right effect). Does anyone know of (R?) software that can do this? Kind regards, Edo Plantinga [[alternative HTML version deleted]]

Hi Edo, you may want to have a look at the R package "rimage" at cran.r-project.org and the software "imagemagick" at www.imagemagick.org If you have a license, Matlab is also very good for such things. Best wishes Wolfgang ------------------------------------- Wolfgang Huber Division of Molecular Genome Analysis German Cancer Research Center Heidelberg, Germany Phone: +49 6221 424709 Fax: +49 6221 42524709 Http: www.dkfz.de/abt0840/whuber ------------------------------------- On Mon, 19 Jan 2004, Edo Plantinga wrote: > Dear all, > > At our department we have experienced some difficulties with our > microarray scanner. I am looking for some software that can read in the > raw TIFF files that come out of our scanner to asses how blurry the > picture is (i.e. how sharp the edges are in the picture). I would also > like to know which areas of the picture are the most blurry (we suspect > a left to right effect). Does anyone know of (R?) software that can do > this? > > Kind regards, > > Edo Plantinga > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor >

On Tue, 20 Jan 2004, Edo Plantinga wrote: > Thank you for your reply. Unfortunately I am using a windows system, and > rimage does not support this. Also, Imagemagick does not correctly open the > files that I have. > Some of my collegues have some Matlab experience, however, so I will ask > them for help. Do you happen to have some Matlab code that does the trick > that I am looking for? > Kind regards, > Edo Plantinga Hi Edo, you can use the matlab function "imread" to read TIFF files. I have no code or experience for blurriness assessment. Maybe start by FFT and look at the high frequency end of the spectrum? Or look at the norm of the gradient field? Imagemagick for me is able to convert TIFF into all sorts of formats, for example into PGM (portable imagemaps [1]). 8-bit binary PGM is read by the function read.pnm in the package pixmap, for 16-bit you would need to adapt the function. [1] http://netpbm.sourceforge.net/doc/pgm.html Best wishes Wolfgang ------------------------------------- Wolfgang Huber Division of Molecular Genome Analysis German Cancer Research Center Heidelberg, Germany Phone: +49 6221 424709 Fax: +49 6221 42524709 Http: www.dkfz.de/abt0840/whuber