[Insight-users] ITK for fluorescence microscopy - BioImageXD

Mon May 11 11:04:18 EDT 2009

Thanks Alex - the wiki is only about 2 weeks old, but coming together nicely. 

I feel that a good wiki is important. The greatest need expressed by my bio-colleagues
is the need for understandable documentation. Our image processing and software terminology
is all gobbledygook & gibberish to them, and we need to overcome that barrier. 

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: Badri Roysam [mailto:roysam at ecse.rpi.edu]
Cc: Daniel James White [mailto:white at mpi-cbg.de], Prashanth Ravindran [mailto:prashanth at 100ximaging.com], ITK [mailto:insight-users at itk.org]
Subject: Re: [Insight-users] ITK for fluorescence microscopy - BioImageXD

> hi badri,
> 
> that's great news. I was sure at one point you would, but I did not  
> know when, hence the question mark in my e-mail.
> 
> Farsight seems to have a lot of activity recently and that's great  
> news for everybody working on cell segmentation. Wiki begins to look  
> good.
> 
> alex.
> 
> 
> 
> On May 11, 2009, at 10:14 AM, Badri Roysam wrote:
> 
> > 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 )
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
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> 