Intrinsic Physiology Feature Extractor (IPFX) - tool for computing neuronal features from the intracellular electrophysiological recordings
Reason this release was yanked:
this is a continuous deployment test run
Project description
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.
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