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

[Mario Emmenlauer]

Dear Melissa,

On 08.07.2014 03:22, Melissa Linkert wrote:
> 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.

Thanks for your very quick fix! I will wait for the upcoming 5.0.3 release
and report back afterwards.

All the best,

    Mario



> 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/
> 
>> _______________________________________________
>> ome-users mailing list
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> 
> 

-- 
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             Mobil: +49-(0)151-68108489
Balanstrasse 43                    mailto: mario.emmenlauer * unibas.ch
D-81669 München                          http://www.marioemmenlauer.de/