[Insight-users] ITK for fluorescence microscopy - BioImageXD

[alex gouaillard]

On May 12, 2009, at 8:07 AM, Daniel James White wrote:

>
> On May 12, 2009, at 12:54 PM, alex gouaillard wrote:
>>>
>>> The vtkLSM Reader was a lot of work, because the LMD510 file format
>>> is
>>> a real pig (but at least its fast) ...
>>>
>>> writing file format readers for VTK is a good thing... but better to
>>> put effort into enhancing the
>>> LOCI Bio-Formats java library and use that for microscopy image and
>>> meta data IO.
>>> That way the wheel is not reinvented over and over, and we can all
>>> benefit from each others work more easily.
>>
>> agreed, but I thought that was an ongoing project in the community?
>> I remember a long thread around january about this?
>
> not sure what you mean....
> yes there was a long thread about it...

Sorry, let me explain more in detail.

I agree that writing and maintaining readers is hard. I agree that we  
should collaborate as much as possible in that matter, and in both our  
cases, (well in any case that involves microscopy datasets i guess)  
using bio formats makes a lot of sense.

Now, because of our design / technological choices, we made it  
difficult for us to do that. Namely, we have chosen to go for an all C+ 
+ solution using VTK /  ITK / QT.

As bio format is written in Java, we made it difficult for us to  
leverage it. We ended up in a situation where most of the image  
processing algorithms we were interested in are in ITK (C++), most of  
the visualization is in VTK (C++), and most of the readers in Bio- 
formats (java).

We were thrilled to see that curtis was putting bioformat interfacing  
with ITK as his main priority in January.

alex.
>
>
> for my money, the right thing to do is to develop bio-formats
> and its integration into other projects
> rather than writing the same file readers for every project.
>
>>
>>>
>>>
>>> BXD might well move to java wrapped VTK/ITK from python in the
>>> future,  primarily for platform independence reasons: No 64 Bit
>>> Carbon
>>> on OSX.
>>> That would also allow a direct interface with Fiji-ImageJ , which
>>> would be very cool.
>>
>> Why not using Cocoa instead of carbon if you want 64 bits?
>> Java rapping is interesting on hits own, of course, for other  
>> reasons.
>
> wxPython  (for out GUI) only works with Carbon on OSX,
> and the native wxAqua port of wxWindows/Widgets is nowhere near
> production ready...
>
> so with wxPython on OSX we are stuck with 32 bit,
> unless we make the effort to bring wxAqua up to scratch,
> and thats a big job.
>
> Switching to java might be easier and also have other long term
> benefits,
> as you allude to.
>
> D
>
>
> Dr. Daniel James White BSc. (Hons.) PhD
> Senior Microscopist / Image Visualisation, Processing and Analysis
> Light Microscopy and Image Processing Facilities
> 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 	Fiji is just ImageJ - Batteries  
> Included
> http://www.chalkie.org.uk
> dan at chalkie.org.uk
> ( white at mpi-cbg.de )
>
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