Thanks for the update....
Well still not working, but i tried to see if the problem was coming from
the tiff files.
When I check for the structure of the tif file here is my output:
[EMAIL PROTECTED] Desktop]$ identify image.tif
image.tif[0] TIFF 550x1429 550x1429+0+0 PseudoClass 65536c 16-bit 34.2579mb
1.060u 0:04
image.tif[1] TIFF 550x1429 550x1429+0+0 PseudoClass 65536c 16-bit 34.2579mb
1.010u 0:04
image.tif[2] TIFF 1604x5108 1604x5108+444+100 PseudoClass 65536c 16-bit
34.2579mb 0.950u 0:04
image.tif[3] TIFF 1604x5108 1604x5108+444+100 PseudoClass 65536c 16-bit
34.2579mb 0.510u 0:03
I don't understand why genepix saves 4 layers when i'm just running 1 array.
Ok, maybe genepix is creating 1 layers per channel but i don't really
understand why the layers have different sizes (550x1429 and 1604x5108). The
experiment is only 1 channel array
The output of the base tif file reported only two layers correspondig to the
two dyes.
[EMAIL PROTECTED] Desktop]$ identify BASE/spots.tif
BASE/spots.tif[0] TIFF 1500x1500 1500x1500+0+0 PseudoClass 65536c 16-bit
5.15392mb 0.450u 0:03
BASE/spots.tif[1] TIFF 1500x1500 1500x1500+0+0 PseudoClass 65536c 16-bit
5.15392mb 0.220u 0:02
Do you think the problem comes from genepix when saving into tif files.
I'm going to save separete tif files and see if i can create correct spots
from these.
david vilanova wrote:
Hello,
I have tried with:
PixelSize="10"
ImageOrigin="4440,1000"
I have double checked the image within genepix and the coordinates
(expressed in µm) are correct (gpr file matches with the tiff file). 1µm
correspond to 10pixels in genepix.
I think it is the other way around. Each pixel is 10µm in size.
See
http://www.moleculardevices.com/pages/software/gn_genepix_file_formats.html#gpr
X Offset: 4400
Y Offset: 1000
X and Y scale: 10
Spot size: try 32; this is given in pixels
However the spot image is not the expected one. Still getting black
squares and sometimes getting spots but a large set of spots instead of
only one. Is a zoom applied to the spot that should be seen , otherwise
i gets hards to view !??
As stated before the pixel coordinates are calculated as:
pixelX = (rawX - offsetX) / scaleX
and the same for the Y coordinates.
It looks like soemthing is wrong and i don't know where to look ? Could
I get your gpr file and tiff image to try and see how it works ??
If you go to http://base.thep.lu.se/browser/trunk/src/test/data
you will find everything you need.
The file 'spots.tif' is the (two-channel) image and the
'test.rawdata.import.txt' is the corresponding raw data set.
/Nicklas
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