Ephys_extraction Workspace

This workspace packages the upstream EphysExtraction/ codebase together with local analysis scripts, converted data, and outputs used during validation.

Upstream source:

• https://github.com/berenslab/EphysExtraction (see NOTICE.md)

Overview (from upstream README)

• Extract electrophysiological parameters from voltage traces.
• Core scripts:
  • EphysExtraction/ephys_features.py: feature extraction utilities
  • EphysExtraction/ephys_extractor.py: per-cell feature extraction
• Notebooks (data format conversion + sanity checks):
  • GetFeaturesPipeline.ipynb (M1, Tolias lab)
  • GetFeaturesPipeline2.ipynb (Hippocampus, Xiaolong lab)
  • GetFeaturesPipelineL4.ipynb (Layer 4 V1/S1, Tolias lab)
  • GetFeaturesPipelineL4Neurolucida.ipynb (Layer 4 V1)
• Upstream development: Yves Bernaerts (main); Supervisor: Philipp Berens.

Local usage

• For scripted NWB analysis, use run_features_on_nwb.py.
• Usage notes are in user_manual.md.

Installation

1. Create a virtual environment:

python -m venv .venv

2. Activate it:

.\.venv\Scripts\activate

3. Install dependencies:

python -m pip install --upgrade pip
python -m pip install ipfx efel bluepyefe neuroconv nwbinspector pynwb

Before publishing or redistributing, review NOTICE.md and CHANGES.md for attribution and local modifications.