[Insight-users] ITK for fluorescence microscopy - BioImageXD

Tue May 12 08:42:38 EDT 2009

And I'll be in OME user meeting next week. A small world…

Gaëtan

Le 12 mai 09 à 13:38, alex gouaillard a écrit :

> hi badri.
>
> Yes we remember curtis discussion on the mailing list in January. It  
> was really interesting.
>
> I see you put him in copy here, curtis any news on the wrapping (in C 
> ++) and using the IO mechanism in ITK? More specifically, anything  
> we could do to help you?
>
> It's a very small world, we also have peter Sorger next door at  
> harvard sys bio who is the co-founder and VP of glencoe software,  
> and one of the cofounder of OME.
>
> I'm also leaving tonight for Paris, and should see gaethan all day  
> wednesday. We have scheduled to work on supporting more classes in  
> the wrapping process. Even though we are not using wrapping  
> ourselves, it's a nice way to catch problems, and to improve quality  
> of the class wrapped.
>
> Alex.
>
>
> On May 12, 2009, at 6:31 AM, Badri Roysam wrote:
>
>> 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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-- 
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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