[Insight-users] Reading LSM images

[Dan White]

Hi Jesse,

On Feb 13, 2010, at 3:19 AM, insight-users-request at itk.org wrote:

> Message: 1
> Date: Fri, 12 Feb 2010 12:34:42 -0500
> From: Jesse Stokum <jessestokum at gmail.com>
> Subject: [Insight-users] Reading LSM images
> To: ITK mailing list <insight-users at itk.org>
> Message-ID:
> 	<6ceea1f01002120934o487c275v6675894ae6f729c9 at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> I'm trying to use ITK's ImageFileReader to read in LSM format images
> and my code is abruptly throwing exceptions.


just so you know, the Carl Zeiss LSM 510 .lsm file format is a mangles  
multi page tiff format,
wit thumbnail images and lots of metadata in the header.

its pretty complicated, but we do have a format sec from Zeiss...

we also made a LSM reader in the BioImageXD project as a VTK kit,
so you can see how that works from the python rapped code n BioImageXD

and there is the java bio-formats library that can read .lsm.

good luck...

Dan



> 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!

Dr. Daniel James White BSc. (Hons.) PhD
Senior Microscopist / Image Processing and Analysis
Light Microscopy Facility
Max Planck Institute of Molecular Cell Biology and Genetics
Pfotenhauerstrasse 108
01307 DRESDEN
Germany

+49 (0)15114966933 (German Mobile)
+49  (0)351 210 2627 (Work phone at MPI-CBG)
+49  (0)351 210 1078 (Fax MPI-CBG LMF)

http://www.bioimagexd.net		BioImageXD
http://pacific.mpi-cbg.de		Fiji (is just ImageJ - batteries included)
http://www.chalkie.org.uk
dan at chalkie.org.uk
( white at mpi-cbg.de )