[ome-users] bioformats and ITK

[Kishore Mosaliganti]

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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