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

[Mark Hiner]

Hi Kedar,

> Any suggestions on how I might begin to debug the problem?

In your original e-mail you said you'd written this with SCIFIO.. I assume
this was with the SCIFIO-ImageIO C++ API. This is still bound to Bio-Formats
4.4.9
<https://github.com/scifio/scifio-imageio/blob/master/src/CMakeLists.txt#L22>.
If the conversion worked with the latest Bio-Formats command line tools, I
would suggest trying the C++ API again with the 5.0.2 LOCI Tools downloaded
here: http://downloads.openmicroscopy.org/bio-formats/5.0.2/

Hope that fixes things.

- Mark


On Fri, Jul 11, 2014 at 3:23 PM, Kedar Grama <gbkedar at gmail.com> wrote:

> Hi Mark,
>
> I hope your release cycle for ImageJ2 went well. I got an executable from
> people at zeiss to export the images from czi to tiff stacks so I have
> reliable access to my data right now. I would like to help figure out the
> problem that I had emailed you about. I ran just bio-formats from the
> command line and the problem did not recur but I can not be sure that bug
> is on the java side because it was pretty random earlier too. Any
> suggestions on how I might begin to debug the problem?
>
> Thanks,
>
> -Kedar
>
>
> On Thu, Jun 19, 2014 at 3:58 PM, Kedar Grama <gbkedar at gmail.com> wrote:
>
>> 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
>>>>>>
>>>>>
>>>>>
>>>>
>>>
>>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://scif.io/pipermail/scifio/attachments/20140714/432f082b/attachment-0002.html>