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

[Mario Emmenlauer]

Dear Melissa,

On 08.07.2014 08:38, Mario Emmenlauer wrote:
> 
> 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.

I can confirm that the fix works. So far I tested with some hundred
images, but I will continue testing with several thousand images.
If I find problems I'll report back.

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
>>> ome-users at lists.openmicroscopy.org.uk
>>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>>
>>
> 

-- 
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/