[ome-users] Matlab imread() and bfopen() disagree

[Melissa Linkert]

Hi Mario,

> it seems I have a problem reading image pixel data from a MetaXpress
> TIFF file using bfopen with newest Bio-Formats. In below link you can
> find a fully self-contained test case. Just download, extract, and
> start from Matlab the script 'bfopentest'. The test case reads included
> image twice, once with imread and once with bfopen, and compares the
> pixel data (which is then found to be different):
> 
>     http://data.marssoft.de/bfopentest.tar.bz2
> 
> Can you please help? The included Bio-Formats with the test case is not
> necessarily the newest, but I just downloaded and tested with newest
> Bio-Formats as well. I have tried with Matlab R2012b and R2014b. I think
> in this case imread() is right, because at least one other reader I tried
> agrees with imread.

Thank you for catching this problem.

We now have a proposed fix:

http://github.com/openmicroscopy/bioformats/pull/1200

There is not yet an official build with that fix, but I would expect it
to be included in the upcoming 5.0.3 release.

Regards,
-Melissa

On Fri, Jul 04, 2014 at 03:51:00PM +0200, Mario Emmenlauer wrote:
> 
> Dear Bio-Formats Developers,
> 
> it seems I have a problem reading image pixel data from a MetaXpress
> TIFF file using bfopen with newest Bio-Formats. In below link you can
> find a fully self-contained test case. Just download, extract, and
> start from Matlab the script 'bfopentest'. The test case reads included
> image twice, once with imread and once with bfopen, and compares the
> pixel data (which is then found to be different):
> 
>     http://data.marssoft.de/bfopentest.tar.bz2
> 
> Can you please help? The included Bio-Formats with the test case is not
> necessarily the newest, but I just downloaded and tested with newest
> Bio-Formats as well. I have tried with Matlab R2012b and R2014b. I think
> in this case imread() is right, because at least one other reader I tried
> agrees with imread.
> 
> Thanks and all the best,
> 
>     Mario
> 
> 
> 
> 

> A: Yes.
> > Q: Are you sure?
> >> A: Because it reverses the logical flow of conversation.
> >>> Q: Why is top posting annoying in email?
> 
> Mario Emmenlauer BioDataAnalysis            Mobile: +49-(0)151-68108489
> Balanstrasse 43                    mailto: mario.emmenlauer * unibas.ch
> D-81669 Munich                           http://www.marioemmenlauer.de/

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