Latest Data Releases

June 2020

New Data & Analyses: Allen Cell Types Database

  • New mouse dataset with gene expression for 1.1 million cells from the cortex and hippocampus, measured with 10x Genomics Chromium 3' v2. 

  • This new Mouse 10x dataset and the Mouse SMART-seq dataset from Oct 2019 were co-analyzed to produce a joint taxonomy of mouse cell types. Both datasets can be visualized and studied in the Transcriptomics Explorer (10x and SMART-seq).

  • New human dataset: 76,533 nuclei from Primary Motor Cortex, processed with 10x Genomics v3. Cell types and gene expression can be studied in the Transcriptomics Explorer.

New Data: Patch-seq data for multimodal characterization

  • Two new single-cell datasets from experiments based on the patch-seq technique. The human dataset contains 318 cells and the mouse has >3700 cells, with another 600 coming in early July. These morphological, eletrophysiological, and transcriptomic data provide a basis for unifying transcriptomic and morpho-eletric characterizations of cell types. 

Updated Data: Allen Brain Observatory – Visual Coding Neuropixels

  • The Visual Coding Neuropixels data from October 2019 has been re-released in an updated Neurodata Without Borders format. The new format corrects several schema validation problems and implements recommendations from the PyNWB project

  • An updated version of AllenSDK has been released and is required to use with the updated NWB data files.

October 3, 2019

New Data & Tools: Allen Brain Observatory – Visual Coding Neuropixels

  • Spiking activity of nearly 100,000 neurons from wild-type mice and 3 transgenic lines, across a variety of regions in the cortex, hippocampus, and thalamus

  • Demonstrates power of Neuropixels, a new probe that represents a major leap forward in neural recording technology

  • Stimuli are similar to those used for the Visual Coding 2P dataset

  • A key feature of these experiments is simultaneously recording across as many as 8 visual regions, which will enable scientists to study inter-areal neural communication patterns in greater detail than ever before

New Data & Tools: Allen Cell Types Database

  • Expanded public datasets of gene expression and corresponding taxonomies of cell types for both mouse and human

  • Mouse dataset now encompasses 75,000 single cells from the entire cortex and hippocampus, providing the basis for comparative studies of cellular diversity in development, evolution, and diseases

  • Human dataset now encompasses 49,000 nuclei from multiple cortical areas, providing the basis for investigating the cellular diversity across human cortex and directly comparison of cell types with matched regions in mouse

  • Both datasets can be explored in a new Transcriptomics Explorer (mouse and human). New functionality will be continue to be routinely released, including filtering, differential search, and visual comparisons for mouse and human data.

New Data & Tools: Synaptic Physiology

  • Mouse and human datasets of simultaneous patch clamp recordings, accompanied by software tools to explore the data

  • Dataset describes 1368 chemical synapses from mouse primary visual cortex and 363 from human cortex

  • Software tools include online Jupyter notebooks and direct API access for download and manipulation of data

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