DataJoint Elements¶
DataJoint Elements are curated data pipeline modules for neurophysiology experiments. Each Element implements common patterns for specific data modalities and integrates seamlessly with other Elements and custom DataJoint pipelines.
For comprehensive documentation, tutorials, and API reference for each Element, visit the Element's repository.
Background¶
DataJoint Elements was developed as part of an NIH BRAIN Initiative project to disseminate open-source data management tools for neuroscience research.
- Grant: U24 NS116470 — DataJoint Pipelines for Neurophysiology
- Institute: National Institute of Neurological Disorders and Stroke (NINDS)
- Period: September 2020 -- August 2025
- PI: Dimitri Yatsenko, DataJoint
The project compiled and systematized data pipeline designs from leading neuroscience laboratories into a library of reusable modules. These modules automate data ingestion and processing for common experimental modalities including extracellular electrophysiology, calcium imaging, pose estimation, and optogenetics.
DataJoint Elements is listed in the BRAIN Initiative Alliance Resource Catalog (SciCrunch ID: SCR_021894).
Neurophysiology¶
- Element Calcium Imaging
Two-photon and widefield calcium imaging analysis with Suite2p, CaImAn, and EXTRACT.
- Element Array Electrophysiology
High-density probe recordings (Neuropixels) with Kilosort and spike sorting.
- Element Miniscope
Miniscope calcium imaging with UCLA Miniscope and Inscopix systems.
- Element Electrode Localization
Anatomical localization of Neuropixels probe electrodes.
Behavior¶
- Element DeepLabCut
Markerless pose estimation with DeepLabCut.
- Element Facemap
Orofacial behavior tracking with Facemap.
- Element MoSeq
Behavioral syllable analysis with Keypoint-MoSeq.
Stimulation & Imaging¶
- Element Optogenetics
Optogenetic stimulation experiments.
- Element Visual Stimulus
Visual stimulation with Psychtoolbox.
- Element ZStack
Volumetric microscopy with Cellpose segmentation and BossDB integration.
Core Elements¶
- Element Lab
Lab, project, and protocol management.
- Element Animal
Subject and genotype management.
- Element Session
Experimental session management.
- Element Event
Event- and trial-based experiment structure.
- Element Interface
Common utilities for DataJoint Elements.
Citation¶
If you use DataJoint Elements in your research, please cite:
Yatsenko D, Nguyen T, Shen S, Gunalan K, Turner CA, Guzman R, Sasaki M, Sitonic D, Reimer J, Walker EY, Tolias AS. DataJoint Elements: Data Workflows for Neurophysiology. bioRxiv. 2021.