[Insight-users] ITK for fluorescence microscopy - BioImageXD

[alex gouaillard]

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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