david vilanova wrote: > Hi folks, > I finally managed to identify the problem. As i said in my previous > email i tried a tif image with only a signe channel: > > [EMAIL PROTECTED] SPOTS]$ ls * > -rw-r--r-- 1 david bioinfo 9,1M Jan 23 12:19 532.tif > -rw-r--r-- 1 david bioinfo 9,3M Jan 23 12:20 635.tif > -rw-r--r-- 1 david bioinfo 20M Jan 23 12:21 All.tif > > CY5 image > [EMAIL PROTECTED] SPOTS]$ identify 635.tif > 635.tif TIFF 1604x5108 1604x5108+444+100 PseudoClass 65536c 16-bit 9.20849mb > > Cy3 image > [EMAIL PROTECTED] SPOTS]$ identify 532.tif > 532.tif TIFF 1604x5108 1604x5108+444+100 PseudoClass 65536c 16-bit 9.02034mb > > [EMAIL PROTECTED] SPOTS]$ identify All.tif > All.tif[0] TIFF 550x1429 550x1429+0+0 PseudoClass 65536c 16-bit > 19.8007mb 1.540u 0:09 > All.tif[1] TIFF 550x1429 550x1429+0+0 PseudoClass 65536c 16-bit > 19.8007mb 1.450u 0:09 > All.tif[2] TIFF 1604x5108 1604x5108+444+100 PseudoClass 65536c 16-bit > 19.8007mb 1.380u 0:09 > All.tif[3] TIFF 1604x5108 1604x5108+444+100 PseudoClass 65536c 16-bit > 19.8007mb 0.700u 0:08 > > > The experiment is a CY5 channel scan. Well the size of the single CY5 > tif image is (1604*5108). > The same for the CY3 image. > > The multi-image tif file returns 2 sizes (1604*5108 and 550*1429). With > that being said i would say the problem comes from base to handle > multi-file generated by genepix. It seems that base is reading the tif > file sequentially and therefore get wrong coordinates for the Cy5 > channel (base takes 550*1429 whereas the correct coordinates are > 1604*5108). > > I guess this is the problem.
Yes, this explains everything. BASE uses the images in the order they are layered in the TIFF file. I don't know why there are two extra layers i your file. Our multi-image files only have two layers, one for each channel. Maybe the two smaller images are some kind of scaled-down preview images? It would explain that some of your spot images contained a lot of small spots and also that some are totally black since the coordinates fall outside the smaller image. > I would say that at some point base needs to make the difference from > genepix multiple-tiff files and single tif files. > > When I use the single CY5 image everyting works fine !!! > > What do you think ? I would recommend that everyone that has a problem with multi-layered image files also try with single-layer image files. It also seems like you save some disk space if you are using single-layer image files. /Nicklas ------------------------------------------------------------------------- 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]
