[Insight-users] ITK for fluorescence microscopy - BioImageXD

[Daniel James White]

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...

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
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http://www.chalkie.org.uk
dan at chalkie.org.uk
( white at mpi-cbg.de )