[ome-users] bioformats and ITK

[Kishore Mosaliganti]

Hi Mark,

Thank you for the email and invaluable help. The bioformats-itk plugin is
wonderful. I am attaching my script here to help you debug. Let me know if
you have any questions on my script. I am starting with a 5D (XYZTC) image
and trying to write out all the 3D timepoints for the first channel.

Kishore

On Fri, Oct 12, 2012 at 12:19 PM, Mark Hiner <hinerm at gmail.com> wrote:

> Hi Kishore,
>
>  I helped develop the bf-itk-pipe plugin and am investigating your issue
> right now.
>
>  What you're doing seems reasonable, so I'm trying to determine if there's
> a bug in the plugin. My goal is to have some working example code for you
> (and a fix if necessary) by the end of the day.
>
> Thank you for using our plugin! I hope we can get it working for you soon.
>
> - Mark
>
> On Fri, Oct 12, 2012 at 10:54 AM, Kishore Mosaliganti <
> kishoreraom at gmail.com> wrote:
>
>> Dear ITK and OME users,
>>
>> To further elaborate, I figured that this has nothing to do with the
>> itkStreamingImageFilter.
>>
>> Instead, the itkImageFileReader seems to be extracting the same image
>> region although I update the requested region in the BioformatsImageIO
>> class :;
>>
>>     itk::BioFormatsImageIO::Pointer io = itk::BioFormatsImageIO::New();
>>     io->SetIORegion( region ); // doesn't make a difference in terms of
>> image data extracted. Its always from the beginning.
>>
>>     ReaderType::Pointer reader = ReaderType::New();
>>     reader->SetFileName(argv[1]);
>>     reader->SetImageIO(io);
>>     reader->Update();
>>
>> So, my general question is whether the BioformatsImageIO expects the
>> whole LSM image to be loaded into memory before writing it out? I would
>> like to specify small image regions since my LSM is too large to be fully
>> loaded into memory. How else can I stream data from large LSM?
>>
>> Thanks,
>>
>> Kishore
>>
>>
>> On Fri, Oct 12, 2012 at 8:53 AM, Kishore Mosaliganti <
>> kishoreraom at gmail.com> wrote:
>>
>>> Hi all,
>>>
>>> I am trying to use bioformats and itk. I downloaded and compiled
>>> bf-itk-pipe using cmake by linking against ITK 3.2:
>>>
>>>
>>> https://github.com/openmicroscopy/bioformats/tree/develop/components/native/bf-itk-pipe
>>>
>>>
>>> I tested out itkBFImageInfo and ./itkRGBBioFormatsImageIOTest on a few
>>> simple LSM images. It works great and writes out all the associated
>>> metadata and pixel data for the first timepoint.
>>>
>>> My LSM microscopy image is 5D. It is X-Y-Z-Time-Channel. I am interested
>>> in extracting individual timepoints from the LSM file for processing. The
>>> filter seems to be using itkStreamingImageFilter. I set the NumberOfStreams
>>> to 10 but that still seems to still write out only the first image.
>>>
>>> How do I set the output requestion region for an individual timepoint?
>>>
>>> Thank you,
>>>
>>> Kishore
>>
>>
>>
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>>
>>
>
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