Resources

This page points to resources/publications from the Allen Institute to understand the cell type database, models, and other ongoing research! See the official overview here.

Celltypes

1. Technical white paper: methods for the Cell Types database
2. Classification of electrophysiological and morphological neuron types in the mouse visual cortex, Gouwens et al., Jul 2019.
3. Shared and distinct transcriptomic cell types across neocortical areas, Tasic et al., Oct 2018: based on genes

Electrophysiology

1. Technical white paper: methods for tissue processing, electrophysiology data acquisition, and analysis of intrinsic properties

Morphology

1. Technical white paper: methods for histological staining, image acquisition, 3D reconstruction and structure-based categorization

Models

1. Systematic generation of biophysically detailed models for diverse cortical neuron types, Gouwens et al., Feb 2018.
2. Systematic Integration of Structural and Functional Data into Multi-scale Models of Mouse Primary Visual Cortex, Bileh et al., Mar 2020.

Biophysical - Perisomatic

Biophysically realistic, single-neuron models with passive dendrites and active soma.

1. Technical white paper

Biophysical - All Active

Biophysically realistic, single-neuron models with active conductances everywhere.

1. Technical white paper

GLIF

Generalized leaky integrate-and-fire single-neuron models.

1. Technical white paper
2. Generalized leaky integrate-and-fire models classify multiple neuron types, Teeter et al., Feb 2018.

Others

More recent, analysis and network papers.

1. Jia, Xiaoxuan, et al. "Multi-regional module-based signal transmission in mouse visual cortex." Neuron 110.9 (2022): 1585-1598.
2. Nandi, Anirban, et al. "Single-neuron models linking electrophysiology, morphology, and transcriptomics across cortical cell types."Cell Reports 40.6 (2022): 111176.
3. Arkhipov, Anton, et al. "Visual physiology of the layer 4 cortical circuit in silico." PLoS computational biology 14.11 (2018): e1006535.