[vtk-developers] [vtkusers] LSM Reader in ITK / VTK - bio-formats

[Karthik Krishnan]

Dan:

Here at Kitware, we have a proprietary vtkLSMReader,
used in VolView (and unlike ITK's reader, handles multi-channel
LSM's). It also handles compressed LSM's (basically all the
compression formats that TIFF supports). However it does not
bother to parse meta-data.

I'd be happy to add it to VTK CVS (of course under a BSD license).

We would like more support for microscopy formats in VTK/ITK;
there have been requests for it on the ITK and VTK users list, and
addition of these readers would broaden the toolkits' adoption by
folks in microscopy.

I noticed that as a part of vtkBXD:
   https://bioimagexd.svn.sourceforge.net/svnroot/bioimagexd/bioimagexd/trunk/vtkBXD/Processing/
you have:

  1. vtkLSMReader - LSM file formats
  2. vtkLIFReader - Leica's .lif formats

Both the readers would be great additions to VTK.

If you would like to have the readers incorporated into VTK, in
keeping with VTK's quality testing process, we would need test
images from you (both single and multi-channel, compressed and
uncompressed), for regression testing.

Dave Cole and I can help with the cleaning up of the code, merging
the readers and adding it to VTK.

How are you handling the meta-data right now. Do you have a
specialized datastructure to house the same ? ITK has its own
meta-data dictionary. VTK has, for a while been using
vtkMedicalImageProperties. I think it might be time to create a
framework for microscopy meta-data in VTK as well.

Mathieu Malaterre can be reached at mathieu.malaterre at kitware.com .
He left Kitware and is back in Lyon.

Thanks
Regards
-- 
Karthik Krishnan
R&D Engineer,
Kitware Inc.
Ph: 518 371 3971 x119
Fax: 518 371 3971

On Wed, Jul 30, 2008 at 5:03 AM, Dan White <white at mpi-cbg.de> wrote:
> Dear All,
> this message bounced from
> the kitware email address for Mathieu
> so I'll just forward it here(s)
> cheers
> Dan
>
>
> From: Dan White <white at mpi-cbg.de>
> Date: July 29, 2008 7:49:00 PM GMT+02:00
> To: Mathieu Malaterre <mathieu.malaterre at kitware.com>
> Subject: LSM reader - bio-formats
>
>
> Hi Mathieu,
>
> I just saw a post on the ITK list,
> mentioning the LSM reader you have added to ITK.
>
> We also spent a lot of time writing one for VTK,
> as part of BioImageXD project.
>
> We use both VTK and ITK in that project,
> but have kept our vtkLSMReader as part of out vtkBXD external C++ kit.
> You can see it there in our svn repository.
>
> The LSM format is a real pig, as you probably know,
> and extracting all the important meta data is really important for post
> processing those images.
>
> It would probably make sense to merge our code,
> and have a single C++ LSM reader for ITK / VTK?
>
> We finally managed to get our reader to read the compressed LSM files...
> does the itkLSM code handle that?
>
> What do you think about a merge?
>
> Our code is currently GPL, but i think we can move stuff to be under the VTK
> style license without any real hassle.
>
> On the other hand.... for biological image format support,
> we should really all be working with the
> LOCI bio-formats project,
> and getting VTK/ITK to work with that java project..
>
> we already both reinvented the wheel once with the 2 LSM readers....
>
>
> cheers
>
> Dan
>
>
> 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
>
>
> New Mobile Number!!!
>
> +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
> http://www.chalkie.org.uk
> dan at chalkie.org.uk
> ( white at mpi-cbg.de )
>
>
>
>
>
>
>
>
> 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
>
> New Mobile Number!!!
> +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
> http://www.chalkie.org.uk
> dan at chalkie.org.uk
> ( white at mpi-cbg.de )
>
>
>
>
>
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