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

Wed Jul 30 05:54:24 EDT 2008

Hi Gaetan,

thanks for the heads up on the wrap ITK / bio-formats news,
that's very interesting for us in the BioImageXD project!

Speed might be an issue. I notice that the C++ lsm reader
we made is probably  faster than the bio-formats java reader for lsm.

(not sure if a direct comparison can easily be made...
but seems for for big files when i open the same one in BioImageXD
and bio-formats importer in imageJ)

Certainly, efforts in the direction of improved performance and  
compatibility
of Bio-formats and VTK/ITK are the best way to go
for VTK/ITK to be able to read the vast multitude of image data formats
from biology / microscopy, and also read the meta data properly.

I hope we at the BioImageXD project have some time in the future to  
help out with that,
as its in out direct interest to use bio-formats instead of
implementing custom readers for all those diverse file formats.

As for Zeiss using horrible MS dependent formats... I have raised the  
issue with them
many times... and they understand the problem... but they are a big   
and sometimes
very  cautiously moving company.
I don't expect them to adopt and open standard format
as their own standard file format very quickly, even though their  
users are repeatedly asking for it.
They have always been open with the documentation for their file  
formats,
which is great, and much appreciated by 3rd party developers,
but thats not the same as using a sane open standard format like OME- 
XML.

cheers

Dan

On Jul 30, 2008, at 11:21 AM, Gaëtan Lehmann wrote:

>
> 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
>

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 )