= Supplementary material =

This page contains supplementary material for the article:
=== Common Atlas Format and 3D Brain Atlas Reconstructor: Infrastructure for Constructing 3D Brain Atlases ===

Piotr Majka, Ewa Kublik, Grzegorz Furga, Daniel K. Wójcik (2011) submitted 

One of the challenges of modern neuroscience is integrating voluminous data of diferent
modalities derived from a variety of specimens. This task requires a common spatial framework 
that can be provided by brain atlases. The first atlases were limited to two-dimentional presentation of structural data. Recently, attempts at creating 3D atlases have been made to offer navigation within non-standard anatomical planes and improve capability of localization of different types of data within the brain volume.

The 3D atlases available so far have been created using frameworks which make it difficult for other
researchers to replicate the results. To facilitate reproducible
research and data sharing in the field we propose a SVG-based Common
Atlas Format (CAF) to store 2D atlas delineations or other compatible data
and ''3D Brain Atlas Reconstructor'' (3dBAR), software dedicated to automated
reconstruction of three-dimensional brain structures from 2D
atlas data. The basic functionality is provided by 1) a set of parsers
which translate various atlases from a number of formats into the CAF,
and 2) a module generating 3D models from CAF datasets.

This methodology allows for the generation of 3D models in a
reproducible and configurable manner. The users of the software may
also track and review the whole reconstruction process in order to
find and correct errors.
Our workflow allows for manual corrections to be made when
automatic reconstruction is not sufficient.

The software was designed to simplify interoperability with other
neuroinformatics tools by using open file formats (SVG, XML, VRML).
The content can easily be exchanged at any stage of data
processing.  The framework allows for the addition of new public or
proprietary content. Most of the framework was implemented as a Python
module with an API.

==== Following supplementary materials are available: ====

1. [wiki:barSoftwareGUI Description of the graphical user interface]
2. [wiki:barSoftwareCLI Command-line interface manual]
3. [wiki:barSoftwareErrorCorrection Description of vector data processing - typical problems and their solutions.]
4. [wiki:barSoftwareGapFillDetails Detailed description of the gap-filling algorithm]
5.  [wiki:barSoftwareEditingContSl Creation of new structures.]