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Overview

This brain cell database is a survey of biological features derived from single cell data, from human and mouse.

The database contains electrophysiological, morphological, and transcriptomic properties gathered from individual cells, and models simulating cell activity. At this early stage of data generation, survey coverage focused on select areas of cerebral cortex, and thalamic neurons.

Browse electrophysiological response data and reconstructed neuronal morphologies using the Cell Feature Search tool. Transcriptomic data can be accessed through the Download page.

Use the Allen Software Development Kit (SDK) to programmatically access and analyze raw data, and to run models.

Data can be downloaded by selecting individual experiments in the Cell Feature Search tool, by accessing transcriptomic RNA-Seq files via the Download page, or through the Allen SDK or API.

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Mouse Data

Cells are acquired from selected brain areas in adult mouse. Cells are identified for isolation based on transgenic mouse lines harboring fluorescent reporters driven by cell type specific drivers. For electrophysiological and morphological analyses, excitatory cells with layer-enriched expression and inhibitory cells based on classical markers were selected. Brain areas selected for analysis include subregions from visual cortex, motor cortex and anterior lateral motor cortex (ALM), in the secondary motor area (MOs).

For transcriptomic analysis, regional and laminar dissections were performed on specimens from pan-neuronal, pan-excitatory, and pan-inhibitory transgenic lines, to sample comprehensively. Data from the lateral geniculate nucleus (LGd) is also included.

This interactive diagram shows how many cells are available for each data modality (electrophysiology, morphology, transcriptomics) and models. Select a category to view the subset of cells.

Include Transcriptomic Data

Human Data

Cells are acquired from donated brain tissue in the temporal or frontal lobes based on structural annotations described in The Allen Human Brain Reference Atlas. For electrophysiological and morphological analyses in the cortex, cells are selected based on soma shape and laminar location.

For transcriptomic analysis, individual layers of cortex are dissected, and neuronal nuclei are isolated. Laminar sampling is guided by the relative number of neurons present in each layer.

Donor Profiles
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This interactive diagram shows how many cells are available for each data modality (electrophysiology, morphology, transcriptomics) and models. Select a category to view the subset of cells.

Include Transcriptomic Data

About Electrophysiology

Whole cell patch clamp recordings provide basic information about cell firing properties. Recordings are performed using a range of stimulus protocols, including short pulses, long steps, slow ramps, and naturalistic noise to characterize the intrinsic properties of these neurons. Detailed protocols are described in the electrophysiology overview technical whitepaper.

About Morphology

Cell structure informs function and neuronal diversity. To view cell shape, cells are filled with biocytin and serially imaged to visualize their morphologies. Planar images and 3D cell reconstructions can be viewed with the cell's electrophysiology data, or downloaded for offline analysis. Detailed protocols are described in the morphology overview technical whitepaper.

About Transcriptomics

RNA sequencing can provide a transcriptomic profile for each cell. Gene transcripts are isolated, amplified and sequenced, and reads are aligned to a reference genome. RNA expression per gene is reported as an average of transcript isoforms. Data is available for whole cells, and in some cases, isolated from nuclear fractions. For nuclei, a significant proportion of reads align to introns. All data can be downloaded, and detailed protocols are described in the transcriptomics overview technical whitepaper.

About Models

A variety of neuronal models that simulate intrinsic cell properties are available. Models include: generalized leaky integrate-and-fire, biophysically realistic, single-neuron models with passive dendrites and active soma (perisomatic), and with active conductances (all-active). Simulations can be viewed online alongside the measured cell responses, where available. All models can be downloaded, and detailed protocols are described in the technical whitepapers: GLIF, perisomatic, all-active.