Hi Chad, This might be a long shot, but I in BASE 1.2.x the Spot images are generated from the jpg images of the array I think, and not the tiffs.
Are you sure this is not the case in BASE 2.x as well, and that your working on the wrong format ? Best, Kjell tir, 03.04.2007 kl. 19.41 skrev Chad Matsalla: > Greetings! > > I'm having trouble understanding how to create spot images for GenePix tiffs > in BASE 2.2.1. > > We use Genepix. I scanned a two-color slide and then exported the images > using Genepix's 'Export Images' function. I chose 'Single-image TIFF files' > and tried both with TIFF LZW compression and without. > > I uploaded the images and the GPR file into BASE, created a raw bioassay, > and selected 'Create Spot Images'. > > After referring to this post: > http://www.mail-archive.com/basedb-users@lists.sourceforge.net/msg00475.html > > I checked the relevant section of the .gpr and saw this: > "PixelSize=10" > "ImageOrigin=2640, 2160" > "JpegOrigin=3240, 2730" > "ScanRegion=264,216,2148,5688" > > I clicked 'Create Spot Images' and provided the filenames. I then provided: > X Scale: 10 > Y Scale: 10 > X Offset: 2640 > Y Offset: 2160 > Gamma correction: 1.8 > Quality: 0.8 > Spot Size: 32 > > I click 'Create', wait, and rather quickly get this: > java.lang.ClassCastException: [[B > at > com.sun.media.jai.opimage.BandMergeOpImage.shortLoop(BandMergeOpImage.java:3 > 41) > at > com.sun.media.jai.opimage.BandMergeOpImage.computeRect(BandMergeOpImage.java > :199) > at javax.media.jai.PointOpImage.computeTile(PointOpImage.java:977) > at > com.sun.media.jai.util.SunTileScheduler.scheduleTile(SunTileScheduler.java:9 > 12) > at javax.media.jai.OpImage.getTile(OpImage.java:1139) > at com.sun.media.jai.opimage.CropOpImage.getTile(CropOpImage.java:133) > .... > > Can anybody help me understand this error? How can I find spots on these > tiffs? > > Thank you, > > Chad Matsalla > > > ------------------------------------------------------------------------- > Take Surveys. Earn Cash. Influence the Future of IT > Join SourceForge.net's Techsay panel and you'll get the chance to share your > opinions on IT & business topics through brief surveys-and earn cash > http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV > _______________________________________________ > The BASE general discussion mailing list > basedb-users@lists.sourceforge.net > unsubscribe: send a mail with subject "unsubscribe" to [EMAIL PROTECTED] -- Kjell Petersen Senior Scientist Computational Biology Unit Bioinformatics group Bergen Center for Computational Science Department of Informatics Unifob AS University of Bergen ------------------------------------------------------------------------- Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT & business topics through brief surveys-and earn cash http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV _______________________________________________ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject "unsubscribe" to [EMAIL PROTECTED]
