Web Based Exploration of Brain Atlases and Data Collections

BrainBaseWeb is the primary user interface to efficiently browse, retrieve and Visualize 3D images registered to a standard brain template (e.g. confocal microscopy data) and annotated anatomical structures from BrainBase. BrainBaseWeb provides several task-centred semantic and interactive query options:

  • Query functionality
    • Semantic Queries: Full Text Semantic Queries
    • Hierarchical Anatomy Browser
    • Anatomical Queries: Search by staining profile in neuropils
    • Spatial High Staining Queries: Draw an arbitrary Region of Interest and retrieve images with high or similar staining or structure.
    • The "Advanced Search" realizes a set of specialized query interfaces, like neuron similarity search, advanced image staining profile search *)
    • BrainBase Query Language (BQL) using a controlled vocabulary *)
  • Advanced web based visualization
    • Automatically generated 2D previews
    • 2D slice views, different multi planar reformation layouts
    • Fully web-based multi-channel 3D volume rendering and mixed geometry-volume rendering
    • Heatmap generation of arborization overlaps. *)
  • Data export
    • Export Data in .tsv and .csv format
    • Workspace to collect data during your session and to export it in Excel format. *)
  • Reproducible ans shareable query results: Shareable links with persistent status of the web interface 

*) only available in BrainBaseWeb 1.0

BrainBaseWeb 2.0

BrainBaseWeb Screenshot
















BrainBaseWeb 1.0

BrainBaseWeb Screenshot