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Spyglass Workshop 2026

NOTE: This workshop is currently in development and subject to change. Please check back for updates on March 4th, 2026.

A hands-on workshop covering practical scientific computing tools and the Spyglass neuroscience data framework.

Contents

Pre-Workshop Requirements

Please complete all of the following before arriving.

  1. Create a GitHub account if you do not already have one.

  2. Bring laptop. Linux or macOS preferred. Spyglass may have issues on Windows; Windows users are welcome to attend and report any problems they encounter.

  3. Install VS Code and Miniconda (or Mamba, recommended).

  4. Install Spyglass using its installer script:

May take up to 45 minutes on a new machine.

git clone https://github.com/LorenFrankLab/spyglass
cd spyglass
python scripts/install.py --minimal # full install not required

This creates a spyglass conda environment containing Spyglass and its core dependencies.

Skip the database setup step — credentials will be provided on the day.

  1. Verify the install:
conda activate spyglass
python -c "import spyglass; print('OK')"

You should see OK. If you see an ImportError, re-run the installer or ask for help before the workshop day: Chris.Broz[at]ucsf.edu

  1. Brush up on Python basics: functions, classes, for loops, if/else, try/except, and shell commands (pip install, conda activate).

On the Day

1. Fork and clone this repository

Click Fork at the top-right of this page → Create fork, then:

git clone https://github.com/<your-username>/SpyglassWorkshop2026
cd SpyglassWorkshop2026

2. Add the workshop to your Spyglass environment

conda activate spyglass
pip install -e .
pre-commit install

This installs the workshop package and its tools (ruff, pytest, pre-commit, jupytext) into the spyglass environment you set up before the workshop.

3. Open VS Code

code .

When VS Code opens, accept any prompts to install the recommended extensions listed in .vscode/extensions.json. Select the spyglass conda environment as your Python interpreter (Ctrl+Shift+P → Python: Select Interpreter).

Schedule

G6, Hugh Robson Building, University of Edinburgh

Time Session
10:00 – 11:30 Session 1: Tools for Scientific Computing
11:30 – 12:30 Break
12:30 – 14:00 Session 2: Spyglass & DataJoint Infrastructure

Session 1: Tools for Scientific Computing (90 min)

Practical tools and workflows for scientific Python development:

  • Overview of GitHub: repositories, branches, forks, pull requests, and issues
  • Setting up VS Code for Python and Jupyter development
  • Working interactively with Jupyter notebooks
  • Code style and quality tools: ruff (replaces black and isort)
  • Debugging your first installable Python package

Session 2: Spyglass & DataJoint Infrastructure (120 min)

Introduction to relational databases and the Spyglass framework:

  • DataJoint infrastructure: Python–MySQL connection
  • Table tiers and declaration syntax
  • Spyglass design patterns: Parameter, Selection, Analysis, and Merge tables
  • Ingesting data into Spyglass
  • Designing a custom Spyglass pipeline

Resources