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.
ScanImage
Widely used open-source software for controlling laser-scanning microscopes (typically two-photon) for in vivo calcium imaging and photostimulation experiments.
Karel Svoboda Lab, Bernardo Sabatini Lab, Bernardo Sabatini Lab initially by Thomas Pologruto
SpikeGLX
Software by Janelia Research Campus for acquiring and visualizing data from high-channel-count neurophysiology recording systems, especially Neuropixels probes.
Bill Karsh
SpikeInterface
An open-source Python framework designed to unify spike sorting and analysis tools, making it easier to run multiple sorters and compare results.
Samuel Garcia, Alessio Buccino, and Cole Hurwitz
TransnetYX Colony
A commercial animal colony management software designed to streamline research operations, track breeding, manage cages, and ensure compliance.
UCLA Miniscope 4.0
Open-source miniature fluorescence microscope (version 4.0) for in vivo calcium imaging in freely behaving animals.
Aniel Aharoni, Peyman Golshani, Alcino Silva, and Baljit Khakh
VAME (Variational Animal Motion Embedding)
A generative modeling framework for animal pose dynamics, allowing for the analysis, synthesis, and prediction of complex animal behavior.
Kevin Luxem and Pavol Bauer
mLIMS
A web-based laboratory information management system (LIMS) often used for managing mouse colonies, tracking breeding, and organizing experimental data.
mesoscope
Refers to specialized large field-of-view two-photon microscopes. Concept and specific designs by various labs like Janelia (Karel Svoboda, Na Ji), Spencer Smith Lab (UCSB), Mark Schnitzer Lab (Stanford).
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