Metadata-Version: 2.1
Name: ipfx
Version: 1.0.0b2
Summary: Intrinsic Physiology Feature Extractor (IPFX) - tool for computing neuronal features from the intracellular electrophysiological recordings
Home-page: https://github.com/AllenInstitute/ipfx
Author: Allen Institute for Brain Science
Author-email: Marmot@AllenInstitute.onmicrosoft.com
License: UNKNOWN
Keywords: neuroscience,bioinformatics,scientific
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Science/Research
Classifier: License :: Other/Proprietary License
Classifier: Natural Language :: English
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 3.7
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Description-Content-Type: text/markdown
Requires-Dist: h5py (>=2.10.0)
Requires-Dist: matplotlib (>=1.4.3)
Requires-Dist: numpy (>=1.12.1)
Requires-Dist: pandas (>=0.17.0)
Requires-Dist: scipy (>=0.15.1)
Requires-Dist: simplejson (>=3.10.0)
Requires-Dist: pillow
Requires-Dist: argschema
Requires-Dist: allensdk
Requires-Dist: dictdiffer
Requires-Dist: pyabf (<2.3.0)
Requires-Dist: hdmf (<2.0.0,>=1.6.2)
Requires-Dist: pynwb (<2.0.0,>=1.3.1)
Requires-Dist: watchdog
Requires-Dist: pg8000
Requires-Dist: pyYAML (<6.0.0)

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:

```bash
 $ 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.


