[Insight-users] Convert Zeiss .zvi files

Tue Jun 30 11:56:43 EDT 2009

> I'm a little puzzled by the farsight build wiki.  It appears to be nothing more than an 
> ITK build, so what's special about "farsight" that it should be identified as something more than Insight (ITK)?

This FARSIGHT wiki page is not quite complete yet. This project is leveraging codes in ITK (that are largely
designed with radiological imaging in mind) and contributing/adding segmentation and analysis algorithms specific
to biological microscopy of cells and tissues. Feel welcome to browse www.farsight-toolkit.org and direct
any questions to me at any time. Best Wishes,

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: Curtis Rueden [mailto:ctrueden at wisc.edu]
To: Darren Weber [mailto:darren.weber.lists at gmail.com]
Cc: roysam at ecse.rpi.edu, Gaëtan Lehmann [mailto:gaetan.lehmann at jouy.inra.fr], insight-users at itk.org, Kevin Eliceiri [mailto:eliceiri at wisc.edu]
Subject: Re: [Insight-users] Convert Zeiss .zvi files

> Hi Darren,
> 
> I'm a little puzzled by the farsight build wiki.  It appears to be nothing
> > more than an ITK build, so what's special about "farsight" that it should
> be
> > identified as something more than Insight (ITK)?
> >
> 
> FARSIGHT is an effort to provide an image analysis toolkit for microscopy,
> based on ITK. There is an (incomplete) list of modules included in FARSIGHT
> listed at:
> 
>   http://www.farsight-toolkit.org/wiki/Table_of_Contents
> 
> It is still very early days for FARSIGHT, with the SVN repository just
> opening up in recent weeks, so everything is still pretty rough around the
> edges.
> 
> Badri Roysam, the head of the project, can comment further on goals and
> directions if you are interested.
> 
> As for OSX, there are no build instructions (most of the linux instructions
> > might apply, but actually it's a lot more complicated because OSX can an
> > rpath nightmare when it comes to shared libs).  I think the entire
> farsight
> > build wiki could be replaced, for OSX, with a one line MacPorts command:
> >
> > sudo port install InsightToolkit
> >
> > This will probably do everything at all stages identified on this wiki
> > thread:
> >
> 
> As far as compililng ITK, yes, if the MacPorts version of ITK includes the
> CableSWIG stuff with WrapITK. (My understanding is that FARSIGHT needs that
> for its Python interface.)
> 
> There are still more instructions to be written on compiling FARSIGHT
> itself, once all the dependencies are set up.
> 
> http://farsight-toolkit.org/wiki/FARSIGHT_Tutorials/Building_Software
> >
> > The MacPorts system will take care of all the dependencies (cmake, python,
> > cableswig).  Please see this ITK wiki page for more details:
> > http://www.vtk.org/Wiki/ITK_MacPorts_Package_Maintainers
> >
> > Moreover, _please_ link to that page from the farsight tutorial on the
> > build process, it might save everyone a lot of time and headaches (because
> I
> > know just how painful it was to put it all together in MacPorts).
> >
> 
> Noted on the Building_Software page.
> 
> If you need to develop ITK using macports, that might be done too, but it
> > requires a little bit of tweaking on the macports installation process. 
> The
> > macports installation uses several phases and a developer could stop after
> > the build phase.  At that point, you have a complete source tree and a
> > separate build tree.  So you could try this:
> >
> > sudo port build InsightToolkit
> >
> > Then go look in the build tree, under /opt/local/var/macports/build/
> >
> 
> Cool; I saw this note on the ITK_MacPorts_Package_Maintainers page too, so
> hopefully people who care will notice that.
> 
> -Curtis
> 
> On Wed, Jun 24, 2009 at 3:08 PM, Darren Weber
> <darren.weber.lists at gmail.com>wrote:
> 
> >
> > I'm a little puzzled by the farsight build wiki.  It appears to be nothing
> > more than an ITK build, so what's special about "farsight" that it should
> be
> > identified as something more than Insight (ITK)?
> >
> > As for OSX, there are no build instructions (most of the linux
> instructions
> > might apply, but actually it's a lot more complicated because OSX can an
> > rpath nightmare when it comes to shared libs).  I think the entire
> farsight
> > build wiki could be replaced, for OSX, with a one line MacPorts command:
> >
> > sudo port install InsightToolkit
> >
> > This will probably do everything at all stages identified on this wiki
> > thread:
> > http://farsight-toolkit.org/wiki/FARSIGHT_Tutorials/Building_Software
> >
> > The MacPorts system will take care of all the dependencies (cmake, python,
> > cableswig).  Please see this ITK wiki page for more details:
> > http://www.vtk.org/Wiki/ITK_MacPorts_Package_Maintainers
> >
> > Moreover, _please_ link to that page from the farsight tutorial on the
> > build process, it might save everyone a lot of time and headaches (because
> I
> > know just how painful it was to put it all together in MacPorts).
> >
> > If you need to develop ITK using macports, that might be done too, but it
> > requires a little bit of tweaking on the macports installation process. 
> The
> > macports installation uses several phases and a developer could stop after
> > the build phase.  At that point, you have a complete source tree and a
> > separate build tree.  So you could try this:
> >
> > sudo port build InsightToolkit
> >
> > Then go look in the build tree, under /opt/local/var/macports/build/
> >
> > Take care,
> > Darren
> >
> >
> >
> >
> >
> > On Wed, Jun 24, 2009 at 11:55 AM, Curtis Rueden <ctrueden at wisc.edu> wrote:
> >
> >> Hi Darren,
> >>
> >> What's the latest on this project?  Is there a wiki how-to on this?
> >>>
> >>
> >> The project is currently under active development. Currently, the plugin
> >> works with ITK 3.12 on Mac OS X and Linux. Soon it will compile with
> Visual
> >> Studio on Windows as well (pending a commit from me -- and thanks to Alex
> >> Gouaillard for his help tracking down some Windows issues).
> >>
> >> There are a number of improvements I am in the process of making,
> >> including support for RGB and vector images, and dimensions beyond 3D. I
> >> would also like to make the build easier to do, as much as possible at
> >> least.
> >>
> >> You can access the code by checking out the LOCI Software codebase from
> >> SVN:
> >>
> >>   https://skyking.microscopy.wisc.edu/svn/java/trunk
> >>
> >> The relevant components are in components/native/bf-cpp and
> >> components/native/itk-plugin. See the readme.txt files for details.
> Please
> >> note that as of this writing, the skyking server is down due to a
> >> large-scale power outage on the UW-Madison campus (some construction
> mishap,
> >> I think).
> >>
> >> There is also a preliminary set of wiki pages on how to compile the
> plugin
> >> on the FARSIGHT wiki at:
> >>
> >>
> >>
> http://farsight-toolkit.org/wiki/FARSIGHT_Tutorials/Building_Software/Bio-Formats
> >>
> >> Note that you do not actually need to build FARSIGHT to use the ITK
> plugin
> >> as is (the wiki pages are written with the idea that the plugin will be
> used
> >> within FARSIGHT, but there is no requirement to do so). The plugin is
> merely
> >> an ITK ImageIO plugin, and should work with any code that uses
> >> itkImageFileReader.
> >>
> >> Lastly, a bug introduced in ITK CVS five weeks ago (which should be fixed
> >> soon) will prevent the plugin from working properly with image data
> beyond
> >> 2D in certain cases.
> >>
> >> I will keep the list posted on my progress.
> >>
> >> -Curtis
> >>
> >> On Wed, Jun 24, 2009 at 1:48 PM, Darren Weber <
> >> darren.weber.lists at gmail.com> wrote:
> >>
> >>>
> >>>> Curtis is working on making bioformats usable from ITK
> >>>
> >>>
> >>>
> >>> What's the latest on this project?  Is there a wiki how-to on this?
> >>>
> >>> Thanks,
> >>> Darren
> >>>
> >>>
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