In conjunction with the publication of an associated paper in Nature, we have made some minor updates to the Merscope and 10x data sets. In addition, 7 new neighborhood embeddings are now fully explorable in the ABC Atlas:
MapMyCells now features its first human reference data set: Seattle Alzheimer’s Disease Brain Cell Atlas (SEA-AD) MTG - 10x single nucleus RNAseq. It was created from a single nucleus RNA-sequencing (snRNAseq) dataset of ~2.0 million cells profiled (~1.4 million cells after QC) and is hierarchically organized into nested levels of classification: 3 classes, 24 subclasses, and 139 Supertypes.
Map your data against this reference data through a set of three new algorithms: Deep generative mapping, as well as re-trained correlation mapping and hierarchical mapping.
Read the full release notes in the community forums.
The Seattle Alzheimer’s Disease Brain Cell Atlas (SEA-AD) is a consortium focused on gaining a deep molecular and cellular understanding of the early pathogenesis of Alzheimer’s Disease. SEA-AD is a collaboration of the Allen Institute for Brain Science, the University of Washington Alzheimer’s Disease Research Center, and Kaiser Permanente Washington Research Institute.
Using the ABC Atlas, users can explore the largest cell-resolution spatial transcriptomics (MERFISH) data set in human brain to date, which provides accurate spatial annotation and colocalization of cell types in the middle temporal gyrus (MTG) of 24 donors from the SEA-AD cohort. This can be viewed in parallel with the 2.78 million cells collected from MTG and dorsolateral prefrontal cortex (DFC) using single nucleus transcriptomics and multiomics (from 84 donors), and organized into a joint taxonomy to allow exploration of gene expression in the context of cell types and donor metrics.
Processed cell by gene count matrices from 10x single nucleus RNAseq dataset from human middle temporal gyrus (MTG) as part of the Seattle Alzheimer’s Disease Brain Cell Atlas (SEA-AD) project. Data is derived from an aged cohort of donors who span the full spectrum of Alzheimer’s disease severity.
Explore the data
This project contains spatial transcriptomics MERFISH datasets from human brain as part of the Seattle Alzheimer’s Disease Brain Cell Atlas (SEA-AD) project. Data is derived from an aged cohort of donors who span the full spectrum of Alzheimer’s disease severity.
Explore the data
MapMyCells transforms cell types from a concept in publications to a tool for public research. Scientists worldwide can now discover what cell types their transcriptomics and spatial data corresponds with by comparing their data to massive, high-quality reference datasets, including the Allen Institute’s whole mouse brain multi-omics atlas, which was developed as part of the NIH’s Brain Initiative Cell Census Network and is available in Allen Brain Cell Atlas.
One key advantage to MapMyCells is scale: using our cloud-based Brain Knowledge Platform and reference datasets with millions of cells, researchers can provide up to 327 million cell-gene pairs from their own data, which is a huge leap forward for working with whole-brain datasets.
Our latest public beta data release includes updates to the mouse whole-brain data collection with revisions to the cell types taxonomy released earlier this year. This cell type taxonomy is an updated version from bioRxiv preprint https://www.biorxiv.org/content/10.1101/2023.03.06.531121v1.
Mouse whole-brain transcriptomic cell type atlas (Hongkui Zeng)
1.7 million single cell transcriptomes spanning the whole adult mouse brain using 10Xv2 chemistry (WMB-10Xv2)
2.3 million single cell transcriptomes spanning the whole adult mouse brain using 10Xv3 chemistry (WMB-10Xv3)
1687 single cell transcriptomes spanning the whole adult mouse brain using the 10X Multiome chemistry (WMB-10XMulti)
Clustering analysis of 4.0 million single cell transcriptomes spanning the whole adult mouse brain combining the 10Xv2, 10Xv3 and 10XMulti datasets (WMB-10X)
A four level whole adult mouse brain taxonomy of cell types (WMB-taxonomy)
3.9 million cell spatial transcriptomics dataset spanning a single adult mouse brain with a 500 gene panel and mapped to the whole mouse brain taxonomy (MERFISH-C57BL6J-638850)
Definition of 8 cell types neighborhoods and UMAP embeddings for fine grain visualization and analysis of neuronal types within and between brain regions (WMB-neighborhoods)
An updated Allen CCFv3 with additional annotations for layers of Ammon's horns, main olfactory blub and a simplifed 5-level anatomical heirarchy (Allen-CCF-2020)
CCF mapped coordinates for cells in the whole brain spatial transcriptomics dataset (MERFISH-C57BL6J-638850-CCF)
A molecularly defined and spatially resolved cell atlas of the whole mouse brain (Xiaowei Zhuang)
4.2 million cell spatial transcriptomics dataset spanning 147 coronal sections with a 1122 gene panel and mapped to the whole mouse brain taxonomy and Allen CCFv3 (Zhuang-ABCA-1; 2.8 million cells passed cell classification confidence score threshold and displayed in the ABC atlas)
1.9 million cell spatial transcriptomics dataset spanning 66 coronal sections with a 1122 gene panel and mapped to the whole mouse brain taxonomy and Allen CCFv3 (Zhuang-ABCA-2; 1.2 million cells passed cell classification confidence score threshold and displayed in the ABC atlas)
2.1 million cell spatial transcriptomics dataset spanning 23 sagittal sections with a 1122 gene panel and mapped to the whole mouse brain taxonomy and Allen CCFv3 (Zhuang-ABCA-3; 1.6 million cells passed cell classification confidence score threshold and displayed in the ABC atlas)
0.22 million cell spatial transcriptomics dataset spanning 3 sagittal sections with a 1122 gene panel and mapped to the whole mouse brain taxonomy and Allen CCFv3 (Zhuang-ABCA-4; 0.16 million cells passed cell classification confidence score threshold and displayed in the ABC atlas)
The Allen Institute for Brain Science has just released the first dataset unifying cell types and anatomy across the whole mouse brain. We are making these preliminary, pre-publication data available to visualize and explore in the public beta release of our new product, the Allen Brain Cell (ABC) Atlas. To learn more about the data and to download full datasets see the ABC Atlas GitHub page for an overview of all the data including notebooks with examples.
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).
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.
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!
New Data:
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
New Data:
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.brain-map.org 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
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