Allen Institute - Mouse Common Coordinate Framework (CCF)

A 3D reference atlas of the adult mouse brain, providing standardized anatomical coordinates and annotations, crucial for spatial registration and analysis of brain data.

Bonsai

A visual programming language for acquiring, processing, and reacting to data streams in real-time. Widely used in neuroscience for behavioral tracking and experiment control.

Bpod

An open-source, real-time control system for animal behavior experiments. It allows precise timing of stimuli and responses and integrates with various hardware.

DANNCE (3D Aligned Neural Network for Computational Ethology)

A deep learning-based tool for 3D markerless animal pose estimation, particularly effective for tracking multiple animals in complex environments.

DeepLabCut

A popular open-source toolbox for markerless pose estimation of animals in videos, using deep learning to track user-defined body parts.

FISH (Fluorescence In Situ Hybridization)

A molecular technique to visualize and quantify RNA molecules directly in tissue by using fluorescent probes.

Facemap

A Python package for tracking facial movements and expressions in rodents using machine learning, often applied to study behavioral states and responses.

Inscopix Miniscope

Commercial miniature fluorescence microscopes and integrated systems for in vivo calcium imaging and optogenetics in freely moving animals.

Intan Technologies

Designs and manufactures electrophysiology hardware, including amplifier chips, headstages, and data acquisition systems widely used in neuroscience research.

Kilosort

Kilosort features spike sorting with accuracy and speed.

MERFISH (Multiplexed Error-Robust FISH)

An advanced FISH technique that allows for the simultaneous imaging and identification of many different RNA species (hundreds to thousands) in single cells within their native tissue context.

MoSeq (Motion Sequencing)

A machine learning framework for unsupervised discovery and analysis of an animal's behavioral repertoire, identifying an "action grammar" from 3D pose data.