[Insight-users] ITK for fluorescence microscopy - BioImageXD

Mon May 11 15:16:08 EDT 2009

hi badri,

I'm so sorry, this is the unmixing code I was speaking long time ago and that I should have sent you already.

We made some experiments and although it is working very well on most, it is underperforming in the specific application our lab is interested in. 

We were hoping to find time to optimize it before releasing it, but we have since lost that hope. I will send you a tarball containing the mathlab code and the corresponding ITK implementation for you to try *right away*. We would be interested in feedback on how it compares to the unmixing code you are using today. I guess that if we could match the result, it would be of interest for  you to use this code, and to remove one external library dependency, right?

We plan to contribute this to ITK, but we won't be on time for the 3.14 release (in a few weeks). We preferred to focus on transferring the segmentation and tracking algorithms first.

regards,

alex.

-----Original Message-----
From: Badri Roysam [mailto:roysam at ecse.rpi.edu] 
Sent: Monday, May 11, 2009 2:31 PM
To: Gouaillard, Alexandre
Cc: naraya3 at rpi.edu
Subject: Re: [Insight-users] ITK for fluorescence microscopy - BioImageXD

HI Alex, I am interested to learn more about your unmixing method. We'd love
to try it out for our immunology live-cell imaging data.

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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> 