Supported Instruments and Tools

Our team, our customers, and the broader DataJoint community have built pipelines around a wide array of instruments, software, and methodologies for neuroscience and behavioral analysis.

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Histology
Fluorescent Calcium Imaging (Multi-photon & Widefield)
Animal Care
Electrophysiology
Fluorescent Calcium Imaging (Multi-photon)
Transcriptomics
Behavior

NeuroNexus

Designs and manufactures a wide range of neural probes (silicon microelectrodes) for acute and chronic electrophysiology recordings in various research applications.

Electrophysiology

Neuroglancer

A WebGL-based viewer for volumetric and 2D neuroscience data, including image series, segmentations, and meshes. Often used for visualizing large connectomics datasets.

Jeremy Maitin-Shepard,

Electrophysiology

Neuropixels

Ultra-high density probes, offering even more recording sites in a compact area.

Electrophysiology

Nikon (NIS-Elements)

Nikon provides advanced microscopy systems. NIS-Elements is their comprehensive software platform for microscope control, image acquisition, processing, and analysis.

Fluorescent Calcium Imaging (Multi-photon)

OpenEphys

An open-source, modular data acquisition system for electrophysiology. It supports various electrode types and is widely used for recording neural activity.

Josh Siegle, Jakob Voigts

Electrophysiology

Patch-seq

An experimental technique that combines patch-clamp electrophysiology, single-cell RNA sequencing (transcriptomics), and morphological characterization from the same neuron.

Vivien Marx, Cathryn Cadwell

Behavior

Transcriptomics

Plexon Inc.

Provides a comprehensive suite of solutions for electrophysiology research, including data acquisition systems, electrodes, and software for spike sorting and analysis.

Harvey W. Wiggins

Electrophysiology

Prairie View

Software historically associated with Prairie Technologies' multiphoton microscopes (now part of Bruker), used for system control and image acquisition.

Fluorescent Calcium Imaging (Multi-photon)

PyRat

Open-source software for behavioral neuroscience experiments, allowing researchers to design and run complex behavioral tasks for rodents and control associated hardware.

Tulio Fernandes De Almeida, Abner Cardoso Rodrigues*†

Animal Care

Ripple Neuro

Develops and provides advanced neural interfacing and processing systems for research, including data acquisition hardware and software for electrophysiology.

Electrophysiology

SLEAP

An open-source, deep-learning based framework for multi-animal markerless pose tracking, capable of tracking multiple individuals even in complex social interactions.

Talmo Pereira, Murthy Lab & Shaevitz Lab)

Behavior

ScanBox

A commercial modular two-photon microscopy system and software developed by Neurolabware, designed for in vivo optical imaging in neuroscience.

Dario Ringach

Fluorescent Calcium Imaging (Multi-photon)

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