What is the "Virtual RatBrain" ?

The Virtual RatBrain Project formed in 2004 in order to build a repository of peer reviewed 3-D cellular anatomical data of the rat brain, collected at multiple levels and from multiple brain regions, including point-to-point coordinate connections, cell populations of different neurochemical phenotype and dendritic and axonal arborizational patterns. We have developed a centralized database that contains digitized 3-D vectorial data that are integrated into a standardized coordinate space ("Virtual RatBrain"). This database can be accessed by our tools which allow users to visualize and analyse this evolving 3-D dataset. The analytical tools include the investigation of density information, as well as, topological association pattern of different cell populations (convergence and divergence), and 3-D analysis of dendritic and axonal morphometry.

How to use the Virtual Rat Brain?

There is two way to use our existing database:

1., Download our Visualization or analytical tools which are able to communicate with our database and show/analyse the existing rat brain database with the contributed cellular and anatomical data. You will be allowed to choose which dataset or brain region you want to visualize or analyse.

2., Use the search/browse capabilities of this website. You can make searches on the metadata which is submitted by the contributors along with their primary vectorial data. The result of the search is a list of data files each of them is a compartment of the existing virtual rat brain. Then you may open it with our downloadable tools or process it your own way.

How to contribute?

The contribution consist of two steps:

1.,   First you have to sign up in our system. You can do it here

2a.,  In order to contribute with your data you have to download our "Warping Tool" which allows you to co-register your data into our standardized coordinate space by defining reference points in your dataset which corresponds to a list of predefined fiducial markers in the reference brain. The warping tool shows the most recent version of the Virtual RatBrain.

2b.,  If you don't want to co-register your data using our "Warping Tool" you can simply upload your data file to our server. Your data file should contain a few global landmarks of the brain. Single reconstructed cell or cell population without appropriate structural outlines is not acceptable.

You can indicate whether or not you want to make your data public. After you contribute we will check your dataset and do some quality control on it and then make it available for the public. Once your data became public, the users will be able to visualize or analyse with our tools as well as download through our website.

How and where is the data stored ?

We use a special XML format (MorphML) for exchange and store neuroanatomical data. Although we prefer this data format our tools are able to use other proprietary data types such as: Neurolucida, Accustage. We use ORACLE9i for data storage.