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

[Kedar Grama]

Hi Curtis,

I have wrapped the Bioformats tools and am using it for now. I'll let you
know and e-mail the ome-users list if the problem recurs.

Thanks,

-Kedar


On Thu, Jun 19, 2014 at 3:48 PM, Curtis Rueden <ctrueden at wisc.edu> wrote:

> 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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