[ome-users] Phosphorimaging TIFF file Support

[Melissa Linkert]

Hi Pete,

> 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)

Hopefully this thread:

http://lists.openmicroscopy.org.uk/pipermail/ome-users/2014-February/004224.html

clears things up a bit, but for the archives Bio-Formats does reverse
the transformation of .gel pixel values as shown here:

https://github.com/openmicroscopy/bioformats/blob/dev_5_0/components/formats-gpl/src/loci/formats/in/GelReader.java#L122

Bio-Formats can be installed as a plugin for reading files in ImageJ (as
well as other software - see http://www.openmicroscopy.org/site/support/bio-formats5/users/index.html),
and can also be used to convert files to a more standard format, e.g. plain TIFF.

Regards,
-Melissa

On Thu, Feb 20, 2014 at 07:57:53PM +0000, Peter Gerondelis wrote:
> 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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