Latest Data Releases

October 4, 2018

The Allen Brain Atlas now contains more data and has a new look!


New Data: Allen Brain Observatory - Visual Coding

  • Data from ~1,000 experiment sessions have been added; image analysis of ~30,000 additional cells brings this dataset to ~63,000 cells

  • Data includes analysis of 8 additional transgenic mouse lines, including:

    • Cells representing three canonical inhibitory markers: Sst, Vip, Pvalb

    • A new reporter (GCaMP6s, via the Ai94 line) to label a pan-excitatory population driven by the Slc17a7 promoter

    • Deep imaging of cells from cortical Layer 6, using the Ntsr1 transgenic driver line

  • Updates to image processing and temporal alignment:  2-photon frame acquisition timing has been corrected, resulting in image frame timestamp adjustments of 30 ms earlier

    • Note: To access adjusted timestamps for previously released data, NWB files must be re-downloaded. Read the AllenSDK Release Notes for more information.

  • pre-publication manuscript is under review, describing the generation and analysis of data from this project


New Data: Allen Cell Types Database

  • Additional electrophysiological recordings and morphological reconstructions have been gathered for:

    • ~ 50 mouse neurons

    • ~ 100 neurons from human, including ~40 morphological reconstructions and over 100 histological images

  • Additional single cell transcriptomic data from cortex is available for download, including:

    • RNA-Seq data from ~16,000 human nuclei, acquired from primary visual and anterior cingulate areas

    • RNA-Seq data from ~10,000 mouse cells, acquired from primary motor and anterior cingulate areas

    • RNA-Seq data from ~7,000 mouse nuclei, acquired from primary motor areas

June 14, 2018

The Allen Brain Atlas at now contains data for more cells from the mouse cortex in the Cell Types Database and additional cell projection maps in the Allen Mouse Brain Connectivity Atlas. The new RNA-Seq Data Navigator is now launched; this application allows users to explore single-cell transcriptomic data by multiple cell features and offers data analysis visualization tools. Finally, a new browser-based 3D visualization of anatomy and cell projection pathways of the mouse brain is available via the Allen Brain Explorer.


New Data and Tools:  Allen Cell Types Database

  • Additional single cell electrophysiology recordings and morphological reconstructions, with models:

    • Data from 18 additional transgenic mouse lines (37 total lines now available)

    • New mouse data: 867 electrophysiology recordings (1918 total), 193 new morphological reconstructions (456 total)

    • New human data: 31 electrophysiology recordings (310 total), 37 new or improved morphological reconstructions (113 total)

    • New biophysical models available for selected neurons: 875 Generalized Leaky Integrate and Fire (GLIF) models for mouse (3288 total), 40 GLIF models for human (465 total)

  • Additional single cell transcriptomic data:

    • RNA-Seq from mouse visual cortex (VISp), anterior lateral motor cortex (ALM), and lateral geniculate nucleus (LGN)

    • RNA-Seq from macaque LGN

    • RNA-Seq from human LGN

  • New tool: RNA-Seq Data Navigator

    • Allows users to visualize distributions of cells based on data-driven clusters from transcriptional profiles and other cell feature metadata and

    • search for genes based on differential gene expression across multiple cell populations


New Data and Tools: Allen Mouse Brain Connectivity Atlas

  • 84 new anterograde projection data sets, for a total of 2995 axonal pathways mapped

  • New Tool: Web browser version of the Allen Brain Explorer (beta)

    • Visualize and navigate anatomic structures of the adult mouse brain in 3D

    • Visualize axonal projection patterns from the Allen Mouse Connectivity Atlas, mapped to corresponding anatomical structures


New Tool: Allen Adult Mouse Brain Reference Atlas - Web Viewer

  • Fully annotated, 3D interactive reference atlas to navigate anatomic structures of the adult mouse brain