[Insight-users] ITK for fluorescence microscopy - BioImageXD

[Badri Roysam]

Dear All, The farsight toolkit SVN will become open this month. We are working on finalizing the
license model and taking care of various little details.


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: alex gouaillard [mailto:alexandre_gouaillard at hms.harvard.edu]
To: Daniel James White [mailto:white at mpi-cbg.de], Prashanth Ravindran [mailto:prashanth at 100ximaging.com]
Cc: ITK [mailto:insight-users at itk.org]
Subject: Re: [Insight-users] ITK for fluorescence microscopy - BioImageXD


> 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 )
> >
> >
> >
> >
> >
> >
> > _____________________________________
> > Powered by www.kitware.com
> >
> > Visit other Kitware open-source projects at
> > http://www.kitware.com/opensource/opensource.html
> >
> > Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
> >
> > Follow this link to subscribe/unsubscribe:
> > http://www.itk.org/mailman/listinfo/insight-users
> 
> _____________________________________
> Powered by www.kitware.com
> 
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
> 
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
> 
> Follow this link to subscribe/unsubscribe:
> http://www.itk.org/mailman/listinfo/insight-users
>