[Insight-users] Reading LSM images

[Jesse Stokum]

Luis,

Thanks for the quick reply, I really appreciate it. The lsm image
stack that I'm working with are actually all in a single file - which
is why I hesitated to use the ImageSeriesReader for this one. I
suppose I could always split the stack into a series of slices imagej
or something else, but it would be more time efficient to just read in
the entire file. Also, intuitively I think that I would get better
filtering results if I handled it as a 3d image, though I could be
wrong about that. Thanks!

Jesse

On Fri, Feb 12, 2010 at 5:07 PM, Luis Ibanez <luis.ibanez at kitware.com> wrote:
> Hi Jesse,
>
>
> If you have the images in independent files (one file per slice),
> you should use the itk::ImageSeriesReader (instead of the
> itk::ImageFileReader).
>
>
> The LSM reader in ITK should be able to manage three channels
> (three components per pixel).
>
> You will find examples on how to use the ImageSeriesReader
> in the ITK Software Guide
>
>                   http://www.itk.org/ItkSoftwareGuide.pdf
>
> in the chapter "Reading and Writing Images",
>
> and you will find source code examples in the directory:
>
>                           Insight/Examples/IO
>
> in particular, you may find interesting the example:
>
>            RGBImageSeriesReadWrite.cxx
>
> you probably only need to replace there the PNGImageIO
> class with a LSMImageIO class.
>
>
> Please give it a try and let us know if you find any problems.
>
> BTW: I you get any Exceptions, please post to the list
> the *exact* error message that you get from the exception.
>
>
>     Thanks
>
>
>
>           Luis
>
>
>
> -------------------------------------------------------------------------------------
> On Fri, Feb 12, 2010 at 12:34 PM, Jesse Stokum <jessestokum at gmail.com> wrote:
>> I'm trying to use ITK's ImageFileReader to read in LSM format images
>> and my code is abruptly throwing exceptions. The images are three
>> channel, and are ~30 slices. Should I consider them 3d images? Here's
>> the code in my main() I've been trying:
>>
>>        typedef itk::RGBPixel<unsigned char> PixelType;
>>        typedef itk::Image<PixelType, 3> ImageType;
>>
>>        typedef itk::ImageFileReader<ImageType> ReaderType;
>>        typedef itk::LSMImageIO ImageIOType;
>>        typedef itk::ImageFileWriter<ImageType> WriterType;
>>
>>        ReaderType::Pointer reader = ReaderType::New();
>>        ImageIOType::Pointer lsmImageIO = ImageIOType::New();
>>        reader->SetImageIO(lsmImageIO);
>>        reader->SetFileName("Tests.lsm");
>>
>> Are lsm pixels vector pixels? I guess I'm just unsure how to handle
>> this situation. Thanks in advance!
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>