/workflow-array-ephys

Example DataJoint workflow for Neuropixels analysis with Kilosort

Primary LanguageJupyter NotebookMIT LicenseMIT

DataJoint Workflow - Array Electrophysiology

DataJoint Workflow for extracellular array electrophysiology combines multiple DataJoint Elements to process data acquired with a polytrode probe (e.g. Neuropixels, Neuralynx) using the SpikeGLX or OpenEphys acquisition software and processed with MATLAB-based Kilosort or python-based Kilosort spike sorting software. DataJoint Elements collectively standardize and automate data collection and analysis for neuroscience experiments. Each Element is a modular pipeline for data storage and processing with corresponding database tables that can be combined with other Elements to assemble a fully functional pipeline.

To get started, see below for an interactive tutorial on GitHub Codespaces. More information can be found at the Element documentation page.

Experiment flowchart

flowchart

Data pipeline for acute experiment

datajoint

Interactive tutorial

The easiest way to learn about DataJoint Elements is to use the tutorial notebook within a GitHub Codespace. Please follow the steps below for the best experience:

  1. Fork this repository to your GitHub account.

  2. Select the green Code button.

  3. Within the dropdown menu, select the Codespaces tab.

  4. Select the green Create codespace on main button.

  5. The environment is ready when a Visual Studio Code window is rendered within your browser. This takes ~5 minutes the first time being launched, and ~1 minute if you revisit this Codespace.

  6. Navigate to the notebooks directory on the left panel and open the tutorial.ipynb Jupyter notebook. Execute the cells in this notebook to begin your walk through the tutorial.

  7. Once you are done, GitHub will automatically stop the Codespace after 30 minutes of inactivity or you can manually stop the Codespace.

  8. After stopping the Codespace, we recommend deleting the Codespace to save on storage costs, which are free for the first 15 GB-month.

  • If you are new to GitHub and run into any errors, please contact us via email at support@datajoint.com. If you are experienced with GitHub, please create an issue on the upstream repository or issue a pull request with a thorough explanantion of the error and proposed solution.

Please Note:

  • GitHub Codespaces are limited to 120 core-hours per month and 15 GB-month for free users. Once you exceed this limit, you will have to wait for the hours to reset or pay to use Codespaces.