The latest updates to the online public resources available through the Allen Brain Atlas data portal were released
on May 14, 2015. These include new data to existing resources and a new database debut.
New resource: Allen Cell Types Database
The Allen Cell Types Database is a new resource
that presents data and analysis from multiple modalities from single cells to allow users to investigate cell
types in the brain.
This first data release includes profiles of 248 individual cells in the mouse visual cortex. Targeted
sampling of cells was conducted with Cre lines, and electrophysiological recordings were taken from each cell.
A subset of cells also has models of cellular behavior that can be downloaded via the
Allen Software Development Kit. Many
cells also contain morphological image data, some of which have been digitally reconstructed in three
Future data releases will also include gene expression profiles of single cells as well as single cell data from
New Science Vignette: A Taxonomy of Cells
Our second Science Vignette is a dynamic
animation that shows how our research team was able to sort hundreds of cells into taxonomic groups based on
The gene expression data for the approximately 1,600 cells in the animation is also available.
The Case Study uses data not a part of the Allen Cell Types Database, but demonstrates the kind of analysis
that can be conducted on the information contained within the database and on data in future releases.
New Common Coordinate Framework (CCF)
A next-generation Allen Mouse Common Coordinate Framework is being created and integrated into the
Allen Brain Atlas Data Portal. The new CCF was created from
1675 mouse specimens that were shape and intensity averaged, resulting in a 10μm isotropic highly detailed
anatomical template. So far, 185 regions have been annotated directly in three dimensions, including 10 visual
areas. In this release, all adult mouse datasets have been registered to this framework.
Additionally, Brain Explorer
has been updated to include fiber tract visual information to enhance understanding of how projections in the
Allen Mouse Brain Connectivity Atlas extend throughout the brain.
New data: Ivy Glioblastoma Atlas Project (Ivy GAP)
The number of gene expression and pathology-grade images in
Ivy GAP has been increased 60-fold, to
over 22,000 in situ hybridization and 12,000 histology images. The number of patients has also expanded
5-fold to 41, and the clinical data include de-identified reports on radiology, pathology, oncology, genomic
alterations, and epigenetic changes.
This update also contains annotation of anatomic structures of glioblastoma at cellular resolution and new
data about putative cancer stem cells that cause glioblastoma.