Latest Data Release October 19, 2017

The Allen Brain Atlas at www.brain-map.org now contains cells from the human cortex in the Allen Cell Types Database, as well as more cells from the mouse visual system and additional cortical areas. A new version of the Allen Mouse Common Coordinate Framework is available, with more detailed anatomical structures, and new data in the Allen Mouse Brain Connectivity Atlas.

Highlights include:

Allen Cell Types Database

  • Introducing data from human medio-temporal gyrus:
    • Single cell electrophysiology recordings, morphological reconstructions, RNA-Seq transcriptomics
    • Human cell models: generalized leaky integrate-and-fire (GLIF) and perisomatic biophysical simulations
  • Expansion of the mouse cell dataset, with more electrophysiology and morphology data, GLIF models and new Cre lines: Chrna2-Cre_OE25 and Nkx2-1-CreERT2

Updated Allen Brain Reference Atlas resources

  • Integrated portal for all reference atlases in the Allen Brain Atlas
  • Release of the newly updated Allen Mouse Common Coordinate Framework (CCF)
  • Anatomical 3D annotations of 672 brain structures, including fine structures in isocortex, non-cortical gray matter structures, fiber tract delineations
  • "Virtual slice" coronal views in the Allen Brain Reference Atlas viewer

New data and tools: Allen Mouse Brain Connectivity Atlas

  • Anatomical structure quantifications of brain connectivity have been recomputed using the new CCF annotation
  • New anterograde projection data sets, for a total of 2,911 including:
    • Cre driver mice for 147 brain-wide projection maps
    • Cre driver mice for 131 projection maps in visual areas
    • Projection target-defined brain-wide and visual-area data sets
  • Improved data viewer: Display image data and annotated CCF slices together

Note to users of the Allen Mouse Brain Connectivity Atlas and Allen Software Developer Toolkit (SDK): Allen SDK users should be aware that as a result of reprocessing connectivity data for the new CCF annotations, all cached structure summary CSV files, 3D grid volumes, and annotation volumes will need to be re-downloaded. To do so, rename the directory containing your Connectivity manifest and re-run your existing scripts.