[Insight-users] ITK for fluorescence microscopy - BioImageXD

[alex gouaillard]

My bad,

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.

Prashanth, That answer your first question: YES ITK is used and  
helpful for microscopy image analysis. I guess you have four projects  
here with four different approaches but all very complementary in spirit

FarSight:  multiple languages (C, C++, IDL, ...)  and libraries (ITK,  
VTK, ...) wrapped in python. Interface to bio formats and Omero.  
Framework, not application. No public access (yet?) to svn. No  
information on license.

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.

gaethan:  core in C / C++, wrapping in python or Java. Use bio-formats  
from python (and maybe java, with imageJ ?). No application that I'm  
aware of. Most is BSD and transfered to ITK.

gofigure: core in C++. Uses ITK / VTK / Qt. Application with plugin  
mechanism. Support Database Back-end. Should support bio-formats and  
Omero in a close future. BSD, and most features are transfered to  
ITK / VTK.

My understanding is that you start from the hardware part, and you're  
already using a lot of java, and ImageJ. I have no experience with  
Java here, but I guess you could ask some question to Gaethan about it.

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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