[SCIFIO] Scrambled tiles in czi files with Scifio-Itk bridge

[Curtis Rueden]

Hi Kedar,

> I have made montages of the same image in three instances where tiles
> were scrambled and once when it worked.

When you have file-format-specific problems like this, it is very important
to understand at what layer the problem is occurring. Please test with
Bio-Formats 5.0.2 -- e.g., with the command line tools, or in an up-to-date
version of Fiji -- and verify whether you see the same faulty behavior.
Then test with an older version of Bio-Formats [1], too. If the problem
occurs with 5.0.2 on its own, that rules out the SCIFIO-ITK bridge layer as
the culprit, meaning the bug should be reported to the ome-users list [2]
so that the Bio-Formats developers can address it.

Or if the problem truly is with the ITK bridge, then Mark is the best
person to investigate, when he returns from vacation.

Regards,
Curtis

[1] http://downloads.openmicroscopy.org/bio-formats/
[2] http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users/


On Thu, Jun 19, 2014 at 9:20 AM, Kedar Grama <gbkedar at gmail.com> wrote:

> Hi Mark,
>
> I have filed an issue on the github site scifio-itk-bridge. We will work
> around the issue for now.
>
> Thanks,
>
> -Kedar
>
>
> On Thu, Jun 19, 2014 at 8:34 AM, Mark Hiner <hinerm at gmail.com> wrote:
>
>> Hi Kedar,
>>
>>  Just wanted to let you know that I'll be out of the country for two
>> weeks starting tomorrow, and all of my time right now is being spent on the ImageJ2
>> release
>> <http://developer.imagej.net/2014/06/04/imagej-200-release-candidate>.
>>
>>  Would you mind filing this as an issue on the scifio-itk-bridge github
>> site: https://github.com/scifio/scifio-itk-bridge ? That way it won't
>> get lost in my e-mail and I can investigate when I get back.
>>
>> Thanks!
>> - Mark
>>
>>
>> On Wed, Jun 18, 2014 at 2:39 PM, Kedar Grama <gbkedar at gmail.com> wrote:
>>
>>> Hi Mark,
>>>
>>> I used SCIFIO to write czi as a 3d stack of either nrrd or tiffs. I get
>>> tiles that are scrambled and this happens at random. My code to convert the
>>> files is here:
>>>
>>> https://github.com/gbkedar/farsight/blob/IlluminationGraphCuts/IlluminationCorrection/readCziWriteCorrectedTiles.cpp
>>>
>>> I have made montages of the same image in three instances where tiles
>>> were scrambled and once when it worked. The czi file is similar to the one
>>> I sent you in June or July last year. Please let me know if you need the
>>> file that I'm using right now and I'll upload it.
>>>
>>> Thanks,
>>>
>>> -Kedar
>>>
>>
>>
>
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