As Wolfgang says, some of teh software designed for microarray analysis may be useful for this purpose. I used TIGR Spotfinder for some time. It's free and easy to use: http://www.tm4.org/spotfinder.html GenePix is also very good, in some ways it may be better. The grid-finding algorithm is great, although for teh sizes we're talking about here a manual approach would be okay. GenePix requires a license... but it's still functional without one, it just restricts the amount of data you can export. I think it's restricted to teh first 1000 spots, which would be enough for your purposes. http://www.moleculardevices.com/pages/software/gn_genepix_pro.html The sort of data these two tools provide varies, so you can check and see which one gives you more of what you want. Also, as Wolfgang said, I don't think I would want a JPEG image (8-bit resolution). It will work if you can't do better, but if you can capture a 16-bit image (typically TIFF format) that will be best. Incidentally, both Spotfinder and Genepix work with 16-bit TIFF files only... Jose Quoting Wolfgang Huber <huber at="" ebi.ac.uk="">: > Dear Christian, > > such a functionality could certainly be developed on top of EBImage, but > I am not aware of any instances. > > If you have a rectangular grid, then maybe also some of the image > analysis software that was developed for quantitating spotted microarray > images could be adapted to your case? > > Please also note that .jpg may not always be ideal for quantitative > analyses, you most likely want to avoid compression and want to use grey > scale intensities that are proportional to what the CCD camera measured. > > Best wishes > Wolfgang > > ------------------------------------------------------------------ > Wolfgang Huber EBI/EMBL Cambridge UK http://www.ebi.ac.uk/huber > > > >> Hi, >> >> I am looking for a R library that would allow the analysis of images >> of plates with colonies arranged on a regular grid on it, for >> instance 32 rows X 48 columns or other densities. These are typically >> used for large scale screen in yeast genetics and genomics where >> different colonies are plated using a pin tool and growth rate are >> estimated based on colony size or intensity from a .jpg image of the >> plate. Has anyone seen this developed for R/Bioconductor? The >> functions would serve to locate a grid on the plate and then extract >> colony intensities or area, in an approach similar to the analysis of >> microscopy screen available through EBIimage. >> >> Thanks for letting me know, >> >> Christian >> > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > -- Dr. Jose I. de las Heras Email: J.delasHeras at ed.ac.uk The Wellcome Trust Centre for Cell Biology Phone: +44 (0)131 6513374 Institute for Cell & Molecular Biology Fax: +44 (0)131 6507360 Swann Building, Mayfield Road University of Edinburgh Edinburgh EH9 3JR UK -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.