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DataJoint Elements provides an efficient approach for neuroscience labs to create and manage scientific data workflows: the complex multi-step methods for data collection, preparation, processing, analysis, and modeling that researchers must perform in the course of an experimental study. The work is derived from the developments in leading neuroscience projects and uses the DataJoint framework for defining, deploying, and sharing their data workflows.
DataJoint
the open-source framework for data pipelines and automated computational workflows + related documentation, tools, and utilities.
DataJoint Elements
a collection of curated modules for assembling workflows for the major modalities of neurophysiology experiments + related documentation, tools, and utilities.
An overview of the principles of DataJoint workflows and the goals of DataJoint Elements are described in the position paper "DataJoint Elements: Data Workflows for Neurophysiology".
| DataJoint Element | Example workflow | Background, Features, and Status | Tutorial Video |
|---|---|---|---|
| Lab management | See Session | Link | See Session |
| Animal management | See Session | Link | See Session |
| Experiment Session management | Lab, subject and session management | Link | Link |
| Extracellular array electrophysiology | Neuropixels | Link | Link |
| Calcium imaging | Multiphoton laser scanning | Link | Link |
| Miniscope imaging | UCLA Miniscope | Link | Link |
| DeepLabCut | Workflow for pose tracking | Link | Link |
| Event- and trial-based experiments | Workflow for Neuropixels Workflow for multiphoton laser scanning |
Link | Link |
| Electrode localization for Neuropixels | Workflow for Neuropixels | Link | Link |
| Facemap | Link | ||
| Visual Stimulation | Link | Link |
- DataJoint for Python
- DataJoint for MATLAB
- DataJoint Documentation
- DataJoint Tutorials
- Docker image for MySQL server configured for use with DataJoint
- Pharus — a REST API for interacting with DataJoint databases
- DataJoint LabBook — a front-end web interface for viewing and entering data
- DataJoint SciViz — a low-code framework for building websites for interactive data visualizaion.
- DataJoint CodeBook — interactive online tutorials
DataJoint and DataJoint Elements are supported by NIH grant U24 NS116470 for disseminating open-source software for neuroscience research. Your feedback is essential for continued funding. Your feedback also helps shape the technology development roadmap for the DataJoint ecosystem. Please tell us about your projects by filling out the DataJoint Census.
- If your work uses DataJoint and DataJoint Elements, please cite the respective Research Resource Identifiers (RRIDs) and manuscripts.
DataJoint for Python or MATLAB
Yatsenko D, Reimer J, Ecker AS, Walker EY, Sinz F, Berens P, Hoenselaar A, Cotton RJ, Siapas AS, Tolias AS. DataJoint: managing big scientific data using MATLAB or Python. bioRxiv. 2015 Jan 1:031658. doi: https://doi.org/10.1101/031658
DataJoint (RRID:SCR_014543) - DataJoint for
<Select Python or MATLAB>(version<Enter version number>)
DataJoint Elements
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 Jan 1. doi: https://doi.org/10.1101/2021.03.30.437358
DataJoint Elements (RRID:SCR_021894) - Element
Enter Element name(version<Enter version number>)