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Automated feature extraction using BluePyEfe

This script scans through an input directory (organized in a certain way), find cells and their respective measurements, group cells by protocol and run a BPE feature extraction for all cells belonging to the same protocol.

To run this script the following components are required:

  • input directory contianing data organized in a particular structure
  • protocol.txt files for each measurement
  • config.json
  • output directory: BPE output will be saved here

Input data - directory structure

Inside the input directory following structure is assumed by the script: each cell has a subdirectory under the input directory. Each cell directory has one or more measurement subdirectories. Each measurement subdirectory has measurement files and a protocol.txt that provides the protocol for a given measurement as well as other information. Summary:

input_dir
    cell1_dir
	    meas1_dir
		    - meas1_ch1_file
		    - meas1_ch2_file
		    - protocol.txt
	    meas2_dir
	    ...
    cell2_dir
    ...

Protocol files

These protocol.txt files either have 5 or 6 rows containing the following information in each row:

  • protocol name: unique identifier of protocol; used for grouping
  • channel: which file contains the voltage data; this string is searched for in the measurement filenames)
  • sampling rate (Hz)
  • parameter list: a 3-tuple containing (ton, toff, duration) - needed for BPE
  • amplitudes list: list of current injection amplitudes (pA)
  • missing sweeps list: list of indices of amplitudes for which the measurements are deemed to be unused for some reason

Config JSON

The script requires a config.json that contains further (protocol-unspecific) configuration parameters that are required to run BluePyEfe (e.g.: list of features to be extracted).

How to run the script

The script takes three parameters:

-cp / --config-path: Path to configuration JSON
-ip / --input-path: Root path for input directory containing raw electrophysiological data
-op / --output-path: Directory where BPE feature extraction results should be saved

Example run:

python extract.py -cp ./config_example.json -ip ./input_directory_example -op ./output_directory

To run the script you need to have BluePyEfe installed. If you want to collect global features (e.g.: rheobase current and all features grouped by rheobase current, fI-curve slopes, etc.) please install the following, modified version of BPE: https://github.com/blazma/BluePyEfe