DataJoint Elements for Neurophysiology¶
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. Elements are a collection of curated modules for assembling workflows for several modalities of neurophysiology experiments and are designed for ease of integration into diverse custom workflows. This work is derived from the developments in leading neuroscience projects and uses the DataJoint API for defining, deploying, and sharing their data workflows.
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".
Below are the projects that make up the family of open-source DataJoint Elements:
- Element Calcium Imaging
A data pipeline for calcium imaging microscopy.
- Element Array Electrophysiology
A data pipeline for Neuropixels probes.
- Element Electrode Localization
A data pipeline for electrode localization of Neuropixels probes.
- Element Miniscope
A data pipeline for miniscope calcium imaging.
- Element ZStack
A data pipeline for segmenting volumetric microscopy data with Cellpose, uploading to BossDB, and visualizing with Neuroglancer.
- Element DeepLabCut
A data pipeline for pose estimation with DeepLabCut.
- Element MoSeq
A data pipeline for motion sequencing with Keypoint-MoSeq.
- Element Facemap
A data pipeline for pose estimation with Facemap.
- Element Optogenetics
A data pipeline for managing data from optogenetics experiments.
- Element Visual Stimulus
A data pipeline for visual stimulation with Psychtoolbox.
- Element Lab
A data pipeline for lab management.
- Element Animal
A data pipeline for subject management.
- Element Session
A data pipeline for session management.
- Element Event
A data pipeline for event- and trial-based experiments.
- Element Interface
Common functions for the DataJoint Elements.