[ome-users] Phosphorimaging TIFF file Support

[Peter Gerondelis]

Hi,  I just downloaded imageJ to check it out.  I have a typhoon phosphorimager and sometimes run 64 lane gels that are too complex for the latest GE software to manage.  As such, I still analyze these files with an old computer running imagequant 5.2.  This software will not run on a box that has greater than 512 MB RAM.  Since that box is about 10 years old, I thought I would see how ImageJ could handle.



So since the GE/Former Amersham/Former Molecular Dynamics .gel file format is based on the tiff standard, ImageJ will read .gel files because they are tiff files.  Unfortunately these instruments (Typhoon and Storm) transform the original pixel values by taking their square root and scaling them before

saving them to a .gel file.  When imagej opens a .gel file, it doesn't reverse this transformation making the images appear muted and unsuitable for quantification.  I posted on the ImageJ list and they said "You could try the Bio-Formats plugin, which is supposed to be able to open .gel files."  Can anyone please explain to me if this is true, how does it work (is it an actual plugin to be installed in to ImageJ or a file converter?  In either case, does this compromise the quantitation (i.e. is it lossless)



Best regards,  Pete


Peter Gerondelis, Ph.D.
S Investigator
HIV DPU
RD Infectious Disease R&D

GSK
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