[Insight-users] ITK for fluorescence microscopy - BioImageXD

[Badri Roysam]

Dear Friends, The LOCI Bio-Formats library that you mentioned has been wrapped
for Python access and is being interfaced with ITK by LOCI. They are part of the
farsight project team, by the way.


Badri Roysam
Professor, Department of Electrical, Computer and Systems Engineering
Associate Director, NSF Center for Subsurface Sensing & Imaging Systems (CenSSIS ERC)
Co-Director, Rensselaer Center for Open Source Software
Rensselaer Polytechnic Institute
110 8th Street, Troy, New York 12180-3590, USA.
Office(JEC 7010): 518-276-8067, Assistant: 518-276-8525, Lab(JEC 6308): 518-276-8207, Fax: 518-276-8715
Email: roysam at ecse.rpi.edu, Web: http://www.ecse.rpi.edu/~roysam



----- Original Message -----
From: Daniel James White [mailto:white at mpi-cbg.de]
To: alex gouaillard [mailto:Alexandre_Gouaillard at hms.harvard.edu]
Cc: ITK [mailto:insight-users at itk.org]
Subject: Re: [Insight-users] ITK for fluorescence microscopy - BioImageXD


> Hi Alex,
> 
> >
> > you're welcome. I have to give you guys some kudo in ohloh, you;re  
> > filter really helps. I added some minor features that I will  
> > contribute back to you first when it will be a little more stable (2  
> > months) and then we can move on to make it part of VTK.
> >
> 
> 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.
> 
> 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.
> 
> 
> >>
> >>> BioImageXD: mainly C/C++ and python. Use ITK / VTK / wxWindow /
> >>> wxPython. Intenral support for specific formats (zeiss, leica, ...).
> >>> Application, but i suppose python module could be used
> >>> independently? License GPL which prevents me from reading the code.
> >>>
> >>
> >> really...? Why? You are in academia right?
> >>
> >
> > yes, I am in academia. but here it is not a question of academia vs  
> > private, or non profit vs profit, it s a pure question of licensing.
> >
> > Let's say I want to distribute my code under BSD. We could find many  
> > reasons for that, first to give complete freedom to anybody to use  
> > it the way they want. Second if one day we want to make compony on  
> > too of it (just like 100ximaging is doing now with their original  
> > project), or for transferring to ITK / VTK later.
> >
> > If I read GPL code and then write a code (anytime in the future)  
> > that does the equivalent work, I can never claim to be 100%  
> > independent  of / uninspired by the GPL code, and thus, the  
> > contamination process start, my code must be GPL. two comments here,  
> > of course, this is only the case if someone sue you, but you never  
> > know. Also it would legal for one individual to read the GPL code,  
> > write down the algorithm on a sheet of paper, then pass it over to  
> > another individual that never read the code and would implement the  
> > algorithm from the drawing / diagram on the paper. This is legal,  
> > but a lot of work.
> >
> > So I could read the code, but then, I woudl make my life seriously  
> > more complicated :-
> 
> Thats a bummer......
> pity this legal stuff sometimes gets in the way of working together  
> for common goals....
> 
> Dan
> 
> 
> 
> 
> 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
> http://www.chalkie.org.uk
> dan at chalkie.org.uk
> ( white at mpi-cbg.de )
> 
> 
> 
> 
> 
> 
> 
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