= 3d Brain Atlas Reconstructor =

''Software dedicated to automatic generation of models of 3D brain structures.''

''Supported by an infrastructural grant[[BR]]
from the Polish Ministry of Regional Development[[BR]]
POIG.02.03.00-00-003/09''

[[PageOutline(2-3,,inline,unnumbered)]]

== Project goals ==

1. Creating software dedicated to automated reconstruction of 3D brain models.
   Key features:
       * Generating model of any combination of structures (ie. basing on structures hierarchy),
       * Arbitrary resolution of generated model (depends on source atlas quality only),
       * Exporting models as polygonal mesh or volumetric datasets.
       * Modularity: One 3D model generation module, many wrappers for different input atlases.

2. Support the software with:
       * Own data (ultimate goal),
       * Existing 2D atlases (as training sets).

3. Creating special dataset format
       * Based on SVG format,
       * Adapted for handling representation of brain structures,
       * Supporting brain regions hierarchy,
       * Maximizing possibilities of atlasing systems interoperability.

4. Ultimately, 3D Brain Atlas Reconstructor would be available as an open source project and on-line service.

== Preprint == 

[http://www.neuroinf.pl/Members/danek/homepage/preprints/Article.2011-03-03.3707/getFile "Common Atlas Format and 3D Brain Atlas Reconstructor, the infrastructure for constructing 3D brain atlases"] [[BR]]
by Piotr Majka, Ewa Kublik, Grzegorz Furga, Daniel K. Wójcik (2011) submitted

== 3d Brain Atlas Reconstructor workflow == 

[[Image(3dbar-workflow.png)]]

== Application screenshots ==

[[Image(3dbar_scr1.png)]]

'''Ontology tree'''  (left) allows browsing for structures, select structures for reconstruction or load already reconstructed models. '''Structure selection tab''' (right) displays detailed information about currently reconstructed structure as well as provides reconstruction properties.

[[Image(3dbar_scr2.png)]]

'''Model customization tab''': Reconstructed structures may be previewed before exporting. Furthermore, additional model modifications (smoothing, mesh complexity reduction, etc. ) may be applied.