This is the first public beta release of BioImage Suite 3.0. This has been
in development for about a year and in internal testing at the Yale MRRC
since the beginning of 2009. It is meant as a preview/testing release and
not for ``production'' work at this stage -- handle with care.
To download see the instructions at
http://research.yale.edu/bioimagesuite/forum/index.php?topic=173.msg1020#newThe direct dowload link is
http://bioimagesuite.org/download/Install_beta.htmlKey new features
* New base libraries VTK 5.2/ITK 3.10/GDCM 2.0 all packaged in a single
distribution directory bioimagesuite3_base. The VTK 5.2 libraries allows
for, in particular, the use of 3D Texture Mapping volume rendering if
supported by the hardware.
* New Object Oriented algorithm -- see
http://bioimagesuite.org/public/bis_algorithm.pdf which unifies GUI and command-line code in BioImage Suite. This has now replaced the old
code in the image processing and registration aspects of BioImage Suite
and will progressively be used for the whole of the software. This is a
major restructuring effort. Ultimately all algorithms in BioImage Suite
will be accessible as either (i) part of main applications (ii)
standalone graphical applications or (iii) standalone command line
modules. All three share the exact same code -- in fact the GUI version
has a button ``Show Command Line'' which shows how such an algorithm
could be invoked on the command line.
For example an algorithm (e.g. linear registration) using the exact same
code can be used either in the GUI as usual, or as a command-line tool
(bis_linearintensityregister.tcl) or as a standalone application
(bis_linearintensityregister.tcl -dogui 1). See the pdf file for more details
There are over 50 new command line tools with a much easier command line syntax.
* A first release of the 80/%-complete fMRI Connectivity Toolbox for both
seed-to-image and seed-to-seed connectivity, and assorted pre-processing
tools.
* A first release of the BioImage Suite database tools for connecting both
to an file-based Mysqlite database (included) and a custom Mysql Server
(to be made available in the next beta release). This can also used
extensively to store parameter sets for the new-style algorithm.
* More complete (though not perfect) DICOM handling using GDCM-2
* Lots of little improvements under the hood
* A first release using the freely available MSYS/MINGW toolchain on
MS-Windows (in addition to the standard VS 2008 release). Binary releases
are also provided for Linux (gcc34 32-bit) and Mac OS X (intel 10.4 or later)
We anticipate that this will be the first of 3-4 beta releases over the
next few months as we built towards the first official BioImage Suite 3.0
release. We will begin updating the manual as well during this time-period.
BioImage Suite is supported in part by the NIH/NIBIB under grant R01
EB006494.
Author
