FW: BioImage Suite 2.5 released
Because there seems to be a problem with the mailing list, i forward
this mail.
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From: Xenophon Papademetris [mailto:xenophon.papademetris@yale.edu]
Sent: Wednesday, January 30, 2008 11:18 AM
To: 'Debian Med Project List'
Subject: BioImage Suite 2.5 released
Since there was some discussion (and misunderstandings) on BioImage
Suite posted on Debian-med late last year, I am forwarding on the
release announcement for BioImage Suite 2.5. With some help (and
prodding) of Dominique Belhachemi we have made all the changes necessary
in the source code and config files for this to compile and run OK on
Debian 4.02 (using gcc 4.1.2) – although we have not run the full set
of GUI and regression tests on Debian – this will happen eventually.
Incidentally, BioImage Suite is released under GPL v2 -- if there is a
serious reason for a GPL v3 licensed version we are open to
dual-licensing if this would help.
Regarding incorporating BioImage Suite into Debian as a package, the
sticky point right now is that BioImage Suite relies on vtk 4.4 (which
compiles on Debian just fine by the way). My understanding is that there
is a vtk-5 package in Debian – however the differences between VTK 4.4
and 5.0 are substantial and this cannot be used. We are beginning work
on BioImage Suite 3.0 (there is an internal alpha version) which will
use vtk 5.2 (if that’s what the next version will be called, there is
some debate on this).
Xenios
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The BioImage Suite team (www.bioimagesuite.org) is happy to make
available
the official release 2.5 of BioImage Suite.5. This supplants the 2.0
release (from February 2007) as the official version of BioImage Suite.
Binary versions are made available for:
* MS-Windows (2000/XP/VISTA)
* Mac OS X 10.4 (both intel and powerpc)
* Linux 32-bit
* Linux 64-bit
* FreeBSD
In addition complete source code is made available under the terms of
the
GPL v2.
You may download it from http://bioimagesuite.org/download/Install.html
using the same username and password that can be found at
http://research.yale.edu/bioimagesuite/forum/index.php?topic=88.0
(You must be registered on the forum to access this information.)
In addition we are be teaching a weekly tutorial course on Medical Image
Analysis & BioImage Suite. All handouts/notes from this class are being
made available online at
http://research.yale.edu/bioimagesuite/course/.
New Features over 2.0
--------------------------------
* Mostly complete support for the NIFTI file format -- see
http://nifti.nimh.nih.gov/ for more details on NIFTI.
* More pervasive image objectmap editing (An objectmap is an image in
which
each value represents a different structure). This is now available
both
in the Surface Editor as before, but also in multi-slice editing modes
as
part of the Mosaic Objectmap Editor and Orthogonal Object Map Editor.
* A preview of the BioImage Suite fMRI tools (still in beta format,
being
ported over from the internal version which is based on VTK 4.0 and
not
easily redistributable).
* A new animation tool for recording animations and saving them as a set
of
.jpeg or .tif files for creating movies for presentation.
* Integration with FSL v 4.0. (Previously BioImage Suite required FSL v
3.1). This needs to be downloaded separately -- see
http://www.fmrib.ox.ac.uk/fsl/ -- and be available in your path.
* Integration with the WFU pick atlas -- you need to download this from
www.fmri.wfubmc.edu. Install this either in an adjacent directory to
BioImage Suite (e.g. /usr/local or C:\yale) or set the environment
variable WFUATLASDIR to point to the atlas location.
* A Levelset segmentation module with a version of the Chan-Vese
algorithm
and local modifications.
* A variety of small and large improvements in the underlying
architecture.
We have eliminated the last few pieces of code that could not have been
redistributed under the GPL with "clean" code resulting in BioImage
Suite
becoming a completely open source package for the first time. We
still, however, strongly recommend that the binary releases be
used, as they have been properly tested.
BioImage Suite is supported in part by the National Institutes of Health
(NIH)/National Institute of Biomedical Imaging and Bioengineering
(NIBIB)
under grant R01 EB006494.
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