Rodent Neocortical Micro- and Mesocircuitry Model

Over 4 million neurons comprise the full data-driven computational model of juvenile rat primary somatosensory cortex, released as a 211,712-neuron subset in the open SONATA format. This model integrates detailed neuron morphologies, synaptic locations on dendritic trees, and connectivity algorithms for local and long-range circuits. Version updates include fixes to synapse property mappings and recalibrated thalamic input strengths to better match biological data.

Use Cases

• Simulating cortical network dynamics based on detailed anatomical connectivity and neuron properties.
• Analyzing laminar and topographic connectivity patterns within and between cortical sub-regions.
• Studying the integration of thalamocortical (VPM/POm) input systems in sensory processing.
• Validating connectivity algorithms (e.g., axo-dendritic overlap) against biological data.
• Benchmarking simulation tools and analysis pipelines using the provided SONATA format and exemplary configurations.

Strengths

• Model contains over 4 million neurons in its full version, representing a large-scale biological circuit.
• Synapses are associated with exact dendritic locations and anatomical parameters like spine length.
• Data is formatted in the open, community-standard SONATA format for interoperability.
• Includes exemplary simulation configurations and ion channel mechanism files (.mod) from the accompanying publication.

Limitations

• The publicly released dataset is a 1.5 mm diameter subset (211,712 neurons), not the full model; access to the complete volume requires contacting the authors.
• Specific row counts, column details, and exact file sizes are not provided in the available metadata.
• The 'last updated' field is inconsistently reported across platform entries.

Provenance

Source

École Polytechnique Fédérale de Lausanne (EPFL), authored by James B. Isbister.

Collection Method

Data-driven computational modeling based on biological data from juvenile rat non-barrel primary somatosensory cortex, using established anatomical workflows and connectivity algorithms.

Freshness

Version 3 was released on 04/05/24, indicating recent maintenance and corrections.

Geography

Model based on the Paxinos & Watson rat brain atlas, focusing on non-barrel primary somatosensory cortex (front limb, jaw subregions, dysgranular zone).