[Insight-users] ITK for fluorescence microscopy - BioImageXD

Tue May 12 07:38:12 EDT 2009

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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