New Data & Analyses:
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).
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.?
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.
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
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:
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
The Allen Brain Atlas now contains more data and has a new look!
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.
A?pre-publication manuscript?is under review, describing the generation and analysis of data from?this project
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
The Allen Brain Atlas at?www.?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:?
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:?
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