BrainBase is a database hosting a large collection of confocal microscopy images showing expressions of VT and enhancer trap Gal4 lines generated by Barry Dickson and his group over several years at the Institute of Molecular Pathology Vienna. The public part of BrainBase (see http://brainbase.imp.ac.at) provides access to 12 000 images and around 120 identified neurons annotated on a subset of these images.

BrainBaseWeb and BrainGazer are the two available user interfaces to BrainBase providing customized tools to access, visualize, explore and mine the data in BrainBase.

Special Features

1

Advanced Queries for lines and neurons of interest

Neuron base Search: Query for images/lines expressing a neuron of interest.

Image Based Search: Query for images/lines showing a structure of interest present in a certain query image.

Anatomical Search: Query for lines and neurons with specific staining profiles

2

Detection and exploration of co-expressions and potential connectivity

Query for arborizations and images showing innervations in certain neuropils or user defined regions.

Overlap computations: Quantify overlaps of staining of a set of lines or annotated arborizations of a set of neurons in arbitrary regions.

neuroMap: Fast hypothesis building on potential connectivity of known neurons.

3

Classification and comparison

Classify unknown neurons or find similar known neurons.

Cluster images and neurons based on global or local similarity.