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.
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 !??
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 ??
david vilanova wrote:
Hello,
Following the advise given to emanuel for the generation of the spots, I
went through the example but could'nt manage to create the spots.
Do i have to submit three time the tiff file to create the spots in the
editor (it's asking for jpeg files�. Anyway the jpeg files didn't work,
i was getting "Bad endianness tag (not 0x4949 or 0x4d4d)".
To create spot images you need the TIFF files.
The tiff file worked out by giving only one tiff file to the red
channel. However the images generated to not show the correct spot, even
after setting the scale and offsets according to the definitions in the
gpr file (given by PixelSize and ImageOrigin). The images are black
squares and sometimes they are some spots in the same image.
This is an indication of incorrect values for one or more of the
scale/offset/spot size values. It could also be that the image doesn't
match the raw data set.
Our test data has a GPR file with the following headers:
"PixelSize=5"
"ImageOrigin=0, 0"
Thus, the X and Y scale is 5 and the X and Y offset is 0. The spot size
is not among the headers, but for this data 32 works fine.
Has someone created spots from a gpr file. Could this person detailed:
- What type of file he used (tiff or jpeg). Jpeg didn't work for me
("Bad endianness tag (not 0x4949 or 0x4d4d)")
- What file it did give to red, green and blue channel (if only one
channel has been used do you need to fill the others)
You can choose to give the file to whichever color you like the best. If
you give it to all three colors the spot images will be grey. With
two-channel data you should give one of the images to one color and the
other to another color. If both channels are stored in the same image
file, give the same file to two colors. BASE will pick the first channel
for the first color and the second channel for the second color.
/Nicklas
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