<div>Hi All,</div>
<div>Please check the following web page to get detailed information about what FARSIGHT does.</div>
<div><a href="http://www.farsight-toolkit.org/wiki/Main_Page">http://www.farsight-toolkit.org/wiki/Main_Page</a></div>
<div> </div>
<div>We regularly update these pages. You can follow it from the recent changes and/or "<span class="mw-headline">RECENTLY ADDED PAGES "</span></div>
<div><span class="mw-headline">from the main page. We talk about the modules. For example, if you click on "Edit-based Validation System " <a href="http://www.farsight-toolkit.org/wiki/EVS">http://www.farsight-toolkit.org/wiki/EVS</a></span></div>
<div><span class="mw-headline">You will see that we have some sample images from the programs that we have implemented. When you download the NucleusEditor.exe from our download pages, you should be able to get similar images where we implement ALISA (Actively Linked Integrated Spaces Architecture) which provides multiple views of segmentation object data. From this data it is possible to decide under or oversegmentation, and merge or delete the objects. As you know none of the segmentation algorithms are perfect! This can be done in a group editing fashion in order to save time. Once we have those segmentation results, we create XML files that contain plenty of features about the objects (cells or blood vessels in this case). </span></div>
<div><span class="mw-headline"></span> </div>
<div><span class="mw-headline">It is then possible to do more analysis from these features. For examples, If you use the TissueNets program, you will be able to create biological networks from these XML files. TissueNets will display these types of networks in 3D. The beauty of this is that once you create your kNN networks, you can collect more information from it. Such as what is the average (median) distance from one cell to its neighbors? Is it possible to display pyramidal region? Is it possible to generate histograms from the features of cells? There are many more features.</span></div>
<div><span class="mw-headline"></span> </div>
<div>You can download the FARSIGHT sources from here:</div>
<div>svn://<a href="http://www.openworld.rpi.edu/repos/farsight">www.openworld.rpi.edu/repos/farsight</a></div>
<div> </div>
<div>and build them by using the steps listed here:</div>
<div><a href="http://www.farsight-toolkit.org/wiki/FARSIGHT_HowToBuild">http://www.farsight-toolkit.org/wiki/FARSIGHT_HowToBuild</a></div>
<div> </div>
<div>Alternatively we have win32 executables if you want to give it a fast try:</div>
<div><a href="http://www.farsight-toolkit.org/wiki/Special:FarsightDownloads">http://www.farsight-toolkit.org/wiki/Special:FarsightDownloads</a></div>
<div> </div>
<div>On this webpage you can either get the FARSIGHT installable and install all the modules at once or download each individual modules and try them. Modules are describe briefly here:</div>
<div><a href="http://www.farsight-toolkit.org/wiki/Table_of_Contents"><em>http://www.farsight-toolkit.org/wiki/Table_of_Contents</em></a></div>
<div> </div>
<div>We plan to have more installables for different platforms.</div>
<div> </div>
<div>Please note that these pages are still under construction. </div>
<div>I will be glad to help anybody if you have any questions.</div>
<div>Aytekin</div>
<div> </div>
<div> </div>
<div>----- Original Message -----<br>> Yes, as of today, the FARSIGHT build wiki as written is by and large an ITK build. There is<br>> another page under construction that is much more FARSIGHT specific. We plan to clean up<br>
> all this confusion soon.<br>> <br>> <a href="http://www.farsight-toolkit.org/wiki/FARSIGHT_HowToBuild">http://www.farsight-toolkit.org/wiki/FARSIGHT_HowToBuild</a><br>> <br>> <br>> Badri Roysam<br>> Professor, Department of Electrical, Computer and Systems Engineering<br>
> Associate Director, NSF Center for Subsurface Sensing & Imaging Systems (CenSSIS ERC)<br>> Co-Director, Rensselaer Center for Open Source Software<br>> Rensselaer Polytechnic Institute<br>> 110 8th Street, Troy, New York 12180-3590, USA.<br>
> Office(JEC 7010): 518-276-8067, Assistant: 518-276-8525, Lab(JEC 6308): 518-276-8207, Fax: 518-276-8715<br>> Email: <a href="http://www.itk.org/mailman/listinfo/insight-users">roysam at ecse.rpi.edu</a>, Web: <a href="http://www.ecse.rpi.edu/~roysam">http://www.ecse.rpi.edu/~roysam</a><br>
><br>><br>><br>><i> Hi Darren and All,<br></i>><i> ><br></i>><i> >> Hi Darren,<br></i>><i> >><br></i>><i> >> I'm a little puzzled by the farsight build wiki. It appears to be <br>
</i>><i> >> nothing<br></i>><i> >>> more than an ITK build, so what's special about "farsight" that it <br></i>><i> >>> should be<br></i>><i> >>> identified as something more than Insight (ITK)?<br>
</i>><i> >>><br></i>><i> >><br></i>><i> >> FARSIGHT is an effort to provide an image analysis toolkit for <br></i>><i> >> microscopy,<br></i>><i> >> based on ITK. There is an (incomplete) list of modules included in <br>
</i>><i> >> FARSIGHT<br></i>><i> >> listed at:<br></i>><i> >><br></i>><i> >> <a href="http://www.farsight-toolkit.org/wiki/Table_of_Contents">http://www.farsight-toolkit.org/wiki/Table_of_Contents</a><br>
</i>><i> >><br></i>><i> >> It is still very early days for FARSIGHT, with the SVN repository <br></i>><i> >> just<br></i>><i> >> opening up in recent weeks, so everything is still pretty rough <br>
</i>><i> >> around the<br></i>><i> >> edges.<br></i>><i> >><br></i>><i> >> Badri Roysam, the head of the project, can comment further on goals <br></i>><i> >> and<br></i>><i> >> directions if you are interested.<br>
</i>><i> >><br></i>><i> ><br></i>><i> ><br></i>><i> > I am working with microscopy data also, so I will keep an eye on <br></i>><i> > this while<br></i>><i> > I'm working with this data.<br>
</i>><i> ><br></i>><i> > Have you looked at the BioImageXD development? I wonder if your <br></i>><i> > work will<br></i>><i> > benefit from more collaboration on that front. Although I read in <br>
</i>><i> > another<br></i>><i> > thread that they want to move to java, instead of a python <br></i>><i> > platform. BTW,<br></i>><i> > the MacPort for InsightToolkit wraps in java, but I've not tested <br>
</i>><i> > any of<br></i>><i> > that wrapping to see if it works.<br></i>><i> ><br></i>><i> > I take it that most of the FARSIGHT work will be in python, and the <br></i>><i> > MacPort<br></i>><i> > for InsightToolkit does use WrapITK with python25 (it should be <br>
</i>><i> > fairly easy<br></i>><i> > to provide python26 or python3x wrapping whenever they are reliable or<br></i>><i> > preferred platforms).<br></i>><i> ><br></i>><i> <br></i>><i> Its true that the medium long term plan is to move / rebuild from <br>
</i>><i> scratch BioImageXD using java<br></i>><i> wrapping.<br></i>><i> <br></i>><i> That said the current python version is under very active development <br></i>><i> right now,<br></i>><i> with a release for windows 32 bit comming pretty soon as we fgix the <br>
</i>><i> las bugs.<br></i>><i> <br></i>><i> The OSX version is proving more problematic as we are struggling to get<br></i>><i> py2app to build a working 32bit OSX .app bundle.<br></i>><i> We have a developer on that task, but nay tips would be welcome!<br>
</i>><i> <br></i>><i> ><br></i>><i> ><br></i>><i> ><br></i>><i> >> As for OSX, there are no build instructions (most of the linux <br></i>><i> >> instructions<br></i>><i> >>> might apply, but actually it's a lot more complicated because OSX <br>
</i>><i> >>> can an<br></i>><i> >>> rpath nightmare when it comes to shared libs). I think the entire <br></i>><i> >>> farsight<br></i>><i> >>> build wiki could be replaced, for OSX, with a one line MacPorts <br>
</i>><i> >>> command:<br></i>><i> >>><br></i>><i> >>> sudo port install InsightToolkit<br></i>><i> >>><br></i>><i> >>> This will probably do everything at all stages identified on this <br>
</i>><i> >>> wiki<br></i>><i> >>> thread:<br></i>><i> >>><br></i>><i> >><br></i>><i> >> As far as compililng ITK, yes, if the MacPorts version of ITK <br></i>><i> >> includes the<br>
</i>><i> >> CableSWIG stuff with WrapITK. (My understanding is that FARSIGHT <br></i>><i> >> needs that<br></i>><i> >> for its Python interface.)<br></i>><i> >><br></i>><i> >> There are still more instructions to be written on compiling FARSIGHT<br>
</i>><i> >> itself, once all the dependencies are set up.<br></i>><i> >><br></i>><i> ><br></i>><i> <br></i>><i> in BioImageXD we have ben using custom VTK and ITK builds (using Wrap <br></i>><i> ITK)<br>
</i>><i> and we have custom kits for VTK and ITK that link to those.<br></i>><i> <br></i>><i> We would like to be able to use a mac ports build of VTK and ITK<br></i>><i> as it would make life simpler, but i dint know if that will work for <br>
</i>><i> us or not,<br></i>><i> i never tried.<br></i>><i> <br></i>><i> ><br></i>><i> > Ah, ha. I look forward to learning more about this. Wherever <br></i>><i> > possible,<br></i>><i> > I'll try to provide support for release versions in MacPorts. I <br>
</i>><i> > will need<br></i>><i> > to know more about your development process and dependencies. If you<br></i>><i> > develop with any release version of ITK as a dependency, that will <br></i>><i> > be easy<br>
</i>><i> > to define as a dependency for a FARSIGHT port in MacPorts and it <br></i>><i> > will then<br></i>><i> > inherit all the dependencies of ITK (the InsightToolkit port). For <br></i>><i> > example:<br>
</i>><i> ><br></i>><i> > $ port deps InsightToolkit<br></i>><i> > InsightToolkit has build dependencies on:<br></i>><i> > cmake<br></i>><i> > gmake<br></i>><i> > gawk<br></i>><i> > bison<br>
</i>><i> > InsightToolkit has library dependencies on:<br></i>><i> > xorg-libs<br></i>><i> > ossp-uuid<br></i>><i> > guile<br></i>><i> > tcl<br></i>><i> > python25<br></i>><i> ><br>
</i>><i> > If you have a separate svn and development modules from the ITK cvs, <br></i>><i> > I would<br></i>><i> > assume a new port for FARSIGHT will be required in MacPorts. I should<br></i>><i> > suggest that for any porting system (MacPorts, FreeBSD, Debian, <br>
</i>><i> > etc.), it<br></i>><i> > would be optimal to have a FARSIGHT dependency on a release version <br></i>><i> > of ITK,<br></i>><i> > rather than an entire, customized ITK development tree that needs to <br>
</i>><i> > be<br></i>><i> > built especially for FARSIGHT. (FYI, for example, wxPython packages <br></i>><i> > the<br></i>><i> > entire wxWidgets in its distribution, rather than just a dependency <br>
</i>><i> > on the<br></i>><i> > wxWidgets library, and that's a pain for porting systems.) In other <br></i>><i> > words,<br></i>><i> > if you need to make changes to ITK, it would be preferable to make <br>
</i>><i> > them in<br></i>><i> > the ITK cvs for their next release (ie, make the change upstream). <br></i>><i> > If you<br></i>><i> > have custom code based on ITK, it's preferable to link against the <br>
</i>><i> > release<br></i>><i> > version and subclass or something within your own library path, <br></i>><i> > until you<br></i>><i> > can commit upstream to ITK (I guess BioImageXD may do something like <br>
</i>><i> > this;<br></i>><i> > someday I should put together a MacPort for that project).<br></i>><i> <br></i>><i> for a mac ports of BioImageXD you might want to wait until we have big <br></i>><i> tested and fixed the upcoming version.<br>
</i>><i> Not sure how long that will take, but for now, the OSX version still <br></i>><i> a bit too alpha, and not really even beta.<br></i>><i> <br></i>><i> We are aiming for a production quality release this time.<br>
</i>><i> <br></i>><i> The tricky but will be the custom ITK and VTK C++ kits we have in the <br></i>><i> svn.<br></i>><i> <br></i>><i> I would be very happy to see a mac ports version of BXD in the future.<br>
</i>><i> It hasnt been tested for a X11 build for a very long time.. no idea of <br></i>><i> it works.<br></i>><i> We use Carbon - wxPython for the GUI.<br></i>><i> <br></i>><i> cheers<br></i>><i> <br>
</i>><i> Dan<br></i>><i> <br></i>><i> <br></i>><i> <br></i>><i> <br></i>><i> <br></i>><i> Dr. Daniel James White BSc. (Hons.) PhD<br></i>><i> Senior Microscopist / Image Visualisation, Processing and Analysis<br>
</i>><i> Light Microscopy and Image Processing Facilities<br></i>><i> Max Planck Institute of Molecular Cell Biology and Genetics<br></i>><i> Pfotenhauerstrasse 108<br></i>><i> 01307 DRESDEN<br></i>><i> Germany<br>
</i>><i> <br></i>><i> +49 (0)15114966933 (German Mobile)<br></i>><i> +49 (0)351 210 2627 (Work phone at MPI-CBG)<br></i>><i> +49 (0)351 210 1078 (Fax MPI-CBG LMF)<br></i>><i> <br></i>><i> <a href="http://www.bioimagexd.net/">http://www.bioimagexd.net</a> BioImageXD<br>
</i>><i> <a href="http://pacific.mpi-cbg.de/">http://pacific.mpi-cbg.de</a> Fiji Fiji is just ImageJ - Batteries Included<br></i>><i> <a href="http://www.chalkie.org.uk/">http://www.chalkie.org.uk</a><br></i>><i> <a href="http://www.itk.org/mailman/listinfo/insight-users">dan at chalkie.org.uk</a><br>
</i>><i> ( <a href="http://www.itk.org/mailman/listinfo/insight-users">white at mpi-cbg.de</a> )<br></i>><i> <br></i>><i> <br></i>><i> <br></i>><i> <br></i>><i> <br></i>><i> <br></i>><i> <br></i>><i> <br>
</i>><i> <br></i>><i> <br></i>><i> <br></i>><i> Dr. Daniel James White BSc. (Hons.) PhD<br></i>><i> Senior Microscopist / Image Visualisation, Processing and Analysis<br></i>><i> Light Microscopy and Image Processing Facilities<br>
</i>><i> Max Planck Institute of Molecular Cell Biology and Genetics<br></i>><i> Pfotenhauerstrasse 108<br></i>><i> 01307 DRESDEN<br></i>><i> Germany<br></i>><i> <br></i>><i> +49 (0)15114966933 (German Mobile)<br>
</i>><i> +49 (0)351 210 2627 (Work phone at MPI-CBG)<br></i>><i> +49 (0)351 210 1078 (Fax MPI-CBG LMF)<br></i>><i> <br></i>><i> <a href="http://www.bioimagexd.net/">http://www.bioimagexd.net</a> BioImageXD<br>
</i>><i> <a href="http://pacific.mpi-cbg.de/">http://pacific.mpi-cbg.de</a> Fiji Fiji is just ImageJ - Batteries Included<br></i>><i> <a href="http://www.chalkie.org.uk/">http://www.chalkie.org.uk</a><br></i>><i> <a href="http://www.itk.org/mailman/listinfo/insight-users">dan at chalkie.org.uk</a><br>
</i>><i> ( <a href="http://www.itk.org/mailman/listinfo/insight-users">white at mpi-cbg.de</a> )<br></i>><i> <br></i>><i> <br></i>><i> <br></i>><i> <br></i>><i> <br></i>><i> <br></i>><i> <br></i>><i> <br>
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<div></div><br>-- <br>My web page: <a href="http://www.cs.rpi.edu/~vargua">http://www.cs.rpi.edu/~vargua</a><br>