Jupyter tutorials

Ethoscopy is best used in a Jupyter instance. We provide a pre-baked docker container that comes with multiuser JupyterHub and the ethoscopy package: ethoscope-lab. Ethoscope-lab 1.6 runs a Python 3.12 kernel with ethoscopy 3.0.0 and an R kernel with an installation of rethomics.

One of the biggest advantages of using Jupyter Notebook is that data treatment can be shared publicly in the most readable format. This is a great tool to aid scientific reproducibility and transparency to your publications.

We provide here below several example notebooks, rendered on this site. The notebooks themselves are in the tutorial_notebook folder of the ethoscopy repository, and their example datasets are fetched with etho.download_tutorial_data() (see Installation).

• Tutorial 1 — Overview (notebook)
• Tutorial 2 — HMM (notebook)
• Tutorial 3 — Circadian analysis (notebook)
• Tutorial 4 — Navigating the ethoscope databases (notebook)
• Tutorial 5 — catch22 feature extraction (notebook)
• Tutorial 6 — Exporting to hctsa (MATLAB) (notebook)
• Paper companion notebook (notebook)