[Insight-users] LSM Reader in ITK / VTK - bio-formats

[Gaëtan Lehmann]

Hi Dan,

About bioformats, you may be interested by the small code I made last  
week to use it from python (with wrapitk).

   http://voxel.jouy.inra.fr/darcs/contrib-itk/bioformats/

It uses a very rough approach: it converts a file in a tif format with  
bioformats, read the tif within itk, and change the spacing (which is  
not passed in the tif).
Very rough, but it works :-)

I'm now able to read the awful zvi format without problem :-)

Of course, it would be way better to do the same in C++, so it would  
be usable without python.

Gaëtan


PS: I think that zvi is even worth than LSM — IIRC, it stores VB  
serialized object, and so is nearly unusable on anything excepted M$  
Windows™ without a huge development effort.


Le 30 juil. 08 à 11:03, Dan White a écrit :

> 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 )
>
>
>
>
>
> _______________________________________________
> Insight-users mailing list
> Insight-users at itk.org
> http://www.itk.org/mailman/listinfo/insight-users

-- 
Gaëtan Lehmann
Biologie du Développement et de la Reproduction
INRA de Jouy-en-Josas (France)
tel: +33 1 34 65 29 66    fax: 01 34 65 29 09
http://voxel.jouy.inra.fr  http://www.mandriva.org
http://www.itk.org  http://www.clavier-dvorak.org

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