These
Java-based tools are capable of reading stacks
of polygons described in svg
vector format and arrange them
in 3D space so that the corresponding structures can be viewed and
manipulated
individually. An additional excel file maintains the structure abbreviations
and their mapping to the terminology of databases that provide
supplementary information.
Here in particular we have manually drawn the cortical, striatal, thalamic and amygdaloid structures of the 151 frontal sections from the "Rhesus Monkey Brain in Stereotactic Coordinates" authored by Paxinos and colleagues. After loading the excel and a set of the svg files, the view can be rotated, zoomed and individual brain structures be selected for identification and simple geometric measures.
The abbreviations of the brain structures are
mapped to entities recorded in the CoCoMac
database of primate brain connectivity. Thereby one can retrieve
mapping and
connectivity information for the selected structure as
text or
connecting arrows.
The CoCoMac-Paxinos-3D viewer is based on the Virtual Rat Brain code
and is freely available for download as an
archive
file under the GNU General Public License.
The software is provided 'as is', and we do not take any legal
responsibility for damages to potential copyright or patent
holders.
Further information will be provided with the second edition of the "Rhesus Monkey Brain in Stereotactic Coordinates" atlas (to be published later this year) and in a forthcoming publication (Bezgin et al., submitted).
02/2008 CoCoMac home neuroPI home