This repository contains notebooks and scripts used for exploring and visualizing Allen Institute datasets and related electrophysiology / Patch-seq examples. It collects code and generated figures for cell-type analyses, Patch-seq metrics, and electrophysiology demonstrations.

• Create a Python environment (recommended: venv or conda)
• Install dependencies:

pip install -r requirements.txt

• Run example scripts (from the repository root):

python scripts/run_all_scripts.py
# or run individual scripts under `scripts/` or `scripts/<subfolder>/`

• requirements.txt minimal packages used by notebooks and scripts.
• scripts/ runnable Python scripts that mirror many of the analyses in the notebooks.
• *.ipynb Jupyter notebooks with interactive analysis and plots (see top-level folders like allen_25, cell_type, electroscopy).

This README was populated to provide a concise overview and to embed the project's generated figures (located in the figures/ folder). If you generate new figures, add them to figures/ and update this README or enable a script to regenerate the README automatically.

Below are representative figures generated by scripts and notebooks in this repo. Each image is stored in figures/.

Example histogram of a cell metric across cell types.

Scatter comparing firing rates and an example metric by cell type.

Pairwise comparison of selected features used for cell-type clustering.

Example BYB recording plot used in electrophysiology demonstrations.

Evoked response traces for an oddball experiment.

Spectrogram visualization of an example recording.

Distribution of a key electrophysiology statistic across recordings.

Library size distribution for Patch-seq samples.

Checkpoint signal plot used in tutorial notebooks.

Simple synthetic signal example used by tutorial code.

Example trace from the Brain Observatory demo notebook.

If you add or regenerate figures, please place them in the figures/ folder and consider updating this README to include them. Pull requests with additional examples or small docs are welcome.

This repository contains educational and analysis code. No license file is included in the repo root if you intend to redistribute or publish, add an appropriate LICENSE file.