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
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