Open Microscopy Environment

Hi Melissa,

thanks a lot for your help.
I took care to uncheck all conversions in rawtherapee but the general problem is: even with 8 bit raw data the color interpolation can yield far more than eight bit color information in a 16 bit rgb container.

For that reason i decided to use dcraw for the test conversion in raw mode without any demosaicing in order to get the raw data written in a single layer tiff (the rggb pattern is clearly visible):

C:\Users\knorbert\Downloads\dcraw-9.12-ms-32-bit.exe -D -W -T -6 O:\CT\cr2test2\07.11.2011_NDVI__MG_2697.CR2

then i got the number of gray levels in the tiff file by
data = imread(aFile);
data = double(data);
vals = unique(data);
numvals = numel(vals)

numvals = 6044

bfopen again yields only 8 bit data.

Best regards
Norbert

Hi everybody,

has anybody an idea how to get the bits per pixel of an cr2-file with a different method than the bioformat library?
I use a Canon EOS 450D and i take raw images which should have 16 bits per pixel as the camera gives 14 bit data. I did not find an option which produces raw files with changed bits per pixel.

Using dcraw like this gives the raw data in 16 bit:
C:\Users\knorbert\Downloads\dcraw-9.12-ms-32-bit.exe -D -W -T -6 O:\CT\cr2test2\07.11.2011_NDVI__MG_2697.CR2

Unfortunately Bioformats reads 8 bit data out of the files.

has anyone an idea why not 16 bit data is read?

Thanks for any answer in advance.

Best
Norbert

Hi Norbert,

Thanks for the additional information, and my apologies for not replying sooner.

After some more investigation, we have determined why Bio-Formats returns 8-bit data instead of 16-bit data; the fix will be in the upcoming 4.4 release of Bio-Formats/OMERO.

Regards,
-Melissa

Hi Melissa,

thanks for your answer and your effort. I feared that my question demands additional effort and i am looking forward to the new release.

Best regards
Norbert