Skip to content

gouwens/ipfx

 
 

Repository files navigation

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

About

No description, website, or topics provided.

Resources

License

Stars

Watchers

Forks

Releases

No releases published

Packages

No packages published

Languages

  • Python 99.6%
  • Other 0.4%