IPFX 1.0.0b2

Intrinsic Physiology Feature Extractor (IPFX) - tool for computing neuronal features from the intracellular electrophysiological recordings

Welcome to Intrinsic Physiology Feature Extractor (ipfx)

ipfx is a python 2/3 package for computing intrinsic cell features from electrophysiology data. This includes:

* action potential detection (e.g. threshold time and voltage)
* cell quality control (e.g. resting potential stability)
* stimulus-specific cell features (e.g. input resistance)

This software is designed for use in the Allen Institute for Brain Science electrophysiology data processing pipeline.

Quickstart:

To run:

 $ cd ipfx/ipfx/bin
 $ python pipeline_from_nwb.py input_nwb_file

User must specify the OUTPUT_DIR inside the pipeline_from_nwb.py

Input:

• input_nwb_file: a full path to the NWB file with cell ephys recordings

Output:

• pipeline_input.json: input parameters
• pipeline_output.json: output including cell features
• output.nwb: NWB file including spike times
• log.txt: run log
• qc_figs: index.html includes cell figures and feature table and sweep.html includes sweep figures

Deprecation Warning

We are working towards a 1.0.0 release of ipfx! This will bring some new features, like NWB2 support, along with improvements to our documentation and testing. We will also drop support for

• NWB1
• Python 2

Older versions of ipfx will continue to be available, but may receive only occasional bugfixes and patches.