= Supplementary material =

Web page http://www.3dbar.org/wiki/barServiceSupplement contains the most recent versions of supplementary materials for the article:

== 3D Brain Atlas Reconstructor service - online repository of three-dimensional models of brain structures ==

Piotr Majka(*), Jakub M. Kowalski, Natalia Chlodzinska, Daniel K. Wójcik; (Neuroinformatics 2013, [http://link.springer.com/article/10.1007%2Fs12021-013-9199-9 DOI:10.1007%2Fs12021-013-9199-9])

== ABSTRACT ==

Brain atlases are important tools of neuroscience. Traditionally
prepared in paper book format, more and more commonly they take digital
form which extends their utility. To simplify work with different
atlases, to lay the ground for developing universal tools which could
abstract from the origin of the atlas, efforts are being made to
provide common interfaces to these atlases. 3D Brain Atlas
Reconstructor service (3dBARs) described here is a repository of
digital representations of different brain atlases in CAF format which
we recently proposed and a repository of 3D models of brain structures.
A graphical front-end is provided for creating and viewing the
reconstructed models as well as the underlying 2D atlas data. An
application programming interface (API) facilitates programmatic access
to the service contents from other websites. From a typical
user's point of view, 3dBARs offers an accessible way
to mine publicly available atlasing data with a convenient browser
based interface, without the need to install extra software. For a
developer of services related to brain atlases, 3dBARs supplies
mechanisms for enhancing functionality of other software. The policy of
the service is to accept new datasets as delivered by interested
parties and we work with the researchers who obtain original data to
make them available to the neuroscience community at large. The
functionality offered by the 3dBARs situates it at the core of present
and future general atlasing services tying it strongly to the global
atlasing neuroinformatics infrastructure.

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

1. [wiki:barServiceServiceSyntax Documentation of the Application Programming Interface (API)]
2. Tutorials:
   - [wiki:barServiceUserGuideAccesingRecWizzard How to access the Custom Reconstruction Wizard?]
   - [http://www.3dbar.org/wiki/barServiceUserGuideLabeledVolumes How to use labeled volumes available at 3dBAR on-line service website?]
   - [http://www.3dbar.org/wiki/barServiceUserGuideNeuralSimulation Using atlas data with a result of a realistic neural network simulation.]
   - [http://www.3dbar.org/wiki/barServiceUserGuideDataFormats Recommended software.]
3. Screencasts:
   - [http://www.youtube.com/watch?v=bSzUYO1hWF0&feature=share&list=PL0BA8CA839C7981CB The complete playlist]:
   - [http://youtu.be/bSzUYO1hWF0?hd=1 Selecting an atlas],
   - [http://youtu.be/Nqnm9XE6P9c?hd=1 Displaying atlas details],
   - [http://youtu.be/-ZT7TF-FyYQ?hd=1 Switching the atlas],
   - [http://youtu.be/P3Al20QtDLk?hd=1 Browsing atlas slides],
   - [http://youtu.be/vO4dzBdpWnw?hd=1 3D model preview],
   - [http://youtu.be/wK4995zYJE0?hd=1 Browsing reconstructed models],
   - [http://youtu.be/lb4mdO_H_bc?hd=1 Requesting a custom reconstruction],
   - [http://youtu.be/t75t8s_wUcQ?hd=1 Using the user panel],
   - [http://youtu.be/L4EzPeVomSY?hd=1 Other features of 3D model preview],
   - [http://youtu.be/8vutD0l1iwU?hd=1 Requesting a composite custom reconstruction].
4. [wiki:barServiceTroubleshooting Troubleshooting]


||||||=  Reproducing results from the article  =||
||=  [http://www.3dbar.org/wiki/barServiceUserGuideLabeledVolumes Figure 3]  =||\
||=  [http://www.3dbar.org:8080/getPreview?cafDatasetName=aba2011;structureName=CTX,CNU,BS,CB# Figure 4]  =||\
||=  Figure 5  =||
||  [[Image(wiki:barServiceSupplement:figure_itksnap_src_small.jpg)]]  ||  [[Image(figure_live_preview_small.jpg)]]  ||  [[Image(figure_crw_small.jpg)]]  ||
{{{#!td valign=top
[http://www.3dbar.org/wiki/barServiceUserGuideLabeledVolumes Reproducing Figure 3]:\\
Labeled volume of [http://braininfo.rprc.washington.edu/PrimateBrainMaps/atlas/Mapcorindex.html Macaque's brain] (Bowden et. al. 2003) loaded into \\
[http://www.itksnap.org/pmwiki/pmwiki.php ITK-SNAP] (Yushkevich et. al. (2006).
}}}
{{{#!td valign=top
[http://www.3dbar.org:8080/getPreview?cafDatasetName=aba2011;structureName=CTX,CNU,BS,CB# Reproducing Figure 4]:\\
Models of structures from the Allen Mouse Brain Reference Atlas\\
(http://mouse.brain-map.org/):
 - brain stem,
 - cerebellum,
 - cerebral nuclei,
 - cerebral cortex.
}}}
{{{#!td valign=top
The output from the Custom\\
Reconstruction Wizard according\\
to settings from Figure 5:
 - [http://www.3dbar.org:8080/getReconstructionByKey?id=96571 VRML scene],
 - [http://www.3dbar.org:8080/getReconstructionByKey?id=96570 PNG image],
 - [http://www.3dbar.org:8080/queryJob?id=329 reconstruction job tracking page].
}}}