[Insight-users] [Insight-developers] Bio-Formats integration with VTK/ITK

[Gaëtan Lehmann]

Hi Curtis,


Le 8 janv. 09 à 22:11, Curtis Rueden a écrit :

> QUESTIONS AND DISCUSSION
>
> My goal with this email is to kickstart some discussion about  
> integrating Bio-Formats with VTK/ITK. Specifically, my questions for  
> the community are:
>
> 1) Do others agree that this form of integration is a good idea? Or  
> is there a better way to accomplish the bulleted goals above?

I'm dreaming of this kind of integration since I saw the bioformats  
talk at the OME meeting in Paris a few years ago. The java/c++  
integration looked a bit too difficult to go that way though - that's  
what lead me to produce a very simple wrapper to use bioformats in  
wrapitk to read images: with a java program which uses bioformats, it  
copies the image to a well know format on the disk (tif) and the  
produced file is read in ITK with a standard reader. Of course, there  
are tons of limitations, and it's nothing but performant. We talked a  
bit about improving this wrapper, but this design seems to poor and  
won't let us get the best from bioformats.

So for sure this form of integration is interesting :-)

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

>
>
> 2) I don't know much about ITK or VTK yet. Where is the right  
> integration point? Within ITK, accessible using ImageIOBase/ 
> ImageIOFactory? Or elsewhere? Does VTK/ITK have an appropriate  
> plugin infrastructure?
>

I don't know if VTK has an IO plugin infrastructure, but ITK has one -  
see http://www.itk.org/Wiki/Plugin_IO_mechanisms

> 3) Does anyone have experience using Jace cross-platform? Or does  
> anyone know an open source solution other than Jace for accessing  
> Java API from C++? Unfortunately, WrapITK & CableSwig go the other  
> way -- wrapping C++ code for access from Java -- which is not what  
> we want here.
>
> 4) Any thoughts on the GPL/BSD licensing issue?

As long as it is distributed as a plugin, as you do for imagej, there  
is no problem.
An integration in ITK would let more people use it, but it would  
require to change the license of bioformats. I understand that you  
don't want to do that, so the plugin seems to be the best way to go IMO.

>
> This project is currently my top priority, but I am not a C++ expert  
> and I would greatly appreciate help from anyone in these various  
> communities. Thanks in advance for any comments and replies!
>

That's a great news to see such an implication from the bioformats side!

Regards,

Gaëtan


-- 
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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