[Insight-users] ITK for fluorescence microscopy - BioImageXD

[alex gouaillard]

On May 11, 2009, at 10:14 AM, Daniel James White wrote:

> Hi Alex,
>
>
> On May 11, 2009, at 4:12 PM, alex gouaillard wrote:
>>
>> BioImageXD is also a wonderful application that has a lot of nice
>> features. They also developed an LSM reader which is the most
>> complete LSM reader freely available in the ITK / VTK community.
>> They also went the extra mile to make this LSM reader available
>> under BSD, and we're using it right now. By the way Dan, we are
>> going to release a channel unmixing (FastICA) code in ITK soon. You
>> might be interested in integrating it.
>>
>
> cheers for the props!
> spectral / channel Unmixing might be interesting yes! cheers for the
> hint!

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.

>
>> 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 :-)


alex.

> cheers
>
> Dan
>
>
>>
>> alex.
>>
>>
>>
>>
>> On May 11, 2009, at 3:52 AM, Daniel James White wrote:
>>
>>> Hi  Prashanth ,
>>>
>>> see
>>> www.bioimagexd.net
>>>
>>> it works very well for us.
>>>
>>> If you want to start a project from scratch, then good luck!
>>> If you want to help us extend the functionality of BXD in
>>> collaboration with us,
>>> then you would be very welcome to join the team!
>>>
>>> Its very easy to add ITK functions to ITK,
>>> as you can see how we did ti already in the source code,
>>> and its only a few lines to add for each new class (depending on how
>>> complex the parameters for it etc are)
>>>
>>> We are also doing work here at MPI-CBG on segmentation of bright
>>> field, phase, DIC etc images.
>>>
>>> cheers
>>>
>>> Dan and the BXD team
>>>
>>> On May 9, 2009, at 6:00 PM, insight-users-request at itk.org wrote:
>>>
>>>>
>>>>
>>>> Dear ITK Users-
>>>>
>>>> I am considering using ITK as the basis for a set of tools for
>>>> analysis of fluorescence and bright-field images. I am curious to
>>>> know if others have tried/ are trying it, and if so what their
>>>> feedback is?
>>>>
>>>> Thanks,
>>>> --Prashanth
>>>
>>> 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
>>>
>>>
>>> New Mobile Number!!!
>>>
>>> +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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>>
>
> 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 )
>
>
>
>
>
>
>