hi everyone, A few weeks ago I sent a message to the list regarding image analysis tools for extracting spots from macro arrays (spotted Nylon membranes). My experiences so far with macroarrays has not been great, 1) I haven't found a good image analysis program for extracting the spot intensities reliably (I will summarize this below) and 2) I am not making many biologist friends when I tell them nothing is significant ;^) The programs I evaluated were: SpotFinder: a Java plugin for Jimage at http://www.math.usu.edu/~adele/spotfinder/index.htm Spot: The program advocated by the Speed clique Bzscan: A stand alone java program http://tagc.univ-mrs.fr/bioinformatics/bzscan/ Well Spot failed, I think primarialy because it didn't handle overlapping spots. The spots do difuse and one can get spot overlap. Also Spot is expensive, for the other two the price is right. Spot finder seems to be doing ok. The program could use a lot of improvement, the automatic gridding did not work well on my data, and really couldn't handle shear in the images. But the spot finding algorithm is nice and is based on a spot shape model. It handles diffusion of the spots well. I am going to try and get a student intern to work on it and improve the speed and make the algoritms more robust to errors on the image. If my company lets me, I will release any improvements. Spot finder was hard to get to work "out of the box" I had to change some of the source. I played with BZscan a bit. It was buggy and the interface clumsy (for me). Also when I was having problems I got no reply form the authors and some of the download links are broken on the web page. It is not clear if they are still supporting it. I also had some problems with spotfinder and getting a reply from the author, but to be fair Adele Cutler is on vacation until the 26th of August and I probably wouldn't answer my email either. She did at least set her auto-reply. I did notice in the archives that Anthony Rossini was looking into making an R-package for Jimage. If he is still planning that it makes SpotFinder even more appealing because it can be run from R with not too much modification. Another note is that Claus Ekstrom has a nice paper on spotshape modelling for microarrays. The work is derived from other work by Mats Rudemo and Erik Gustafson on modelling spot shapes on protien gels, which are probably similar to macroarrays. I think they are working on an R package as well which may be useful. Lastly I was reccomended to try Arraypro analyser by Peter Wilkinson (https://stat.ethz.ch/pipermail/bioconductor/2004-July/005533.html) I haven't downloaded the demo yet and tried, sorry. Hope this helps. Nicholas

"Nicholas Lewin-Koh" <nikko@hailmail.net> writes: > I did notice in the archives that Anthony Rossini was looking into > making an R-package for Jimage. For various reasons, I'm not going to be doing that. best, -tony -- Anthony Rossini Research Associate Professor rossini@u.washington.edu http://www.analytics.washington.edu/ Biomedical and Health Informatics University of Washington Biostatistics, SCHARP/HVTN Fred Hutchinson Cancer Research Center UW (Tu/Th/F): 206-616-7630 FAX=206-543-3461 | Voicemail is unreliable FHCRC (M/W): 206-667-7025 FAX=206-667-4812 | use Email CONFIDENTIALITY NOTICE: This e-mail message and any attachme...{{dropped}}