Version 0.7.0a
New in this version:
- Simplified process for analysis of IV/spike data (current clamp IVs). All analyzed data is stored in Python pkl files in cell-specific subdirectories in a "dataset" directory.
- A text-formatted configuration file provides project-specific parameters, colors, lists, directories, etc. This serves both to expose some parameters in the analysis, and to make sure that parameters that get changed are not hidden in the code.
Note that this is "alpha" code, meaning that it works for me, but also that errors may occur that have to be identified and solved.
This is an experimental suite of programs for analyzing electrophysiology data, written in Python. These are not considered appropriate for general use at this point, but may be a useful starting point. In my lab, these are used for various aspects of analysis, and so are actively used and under regular development. A recent refactoring of some of the code (May 2020) may have rendered certain parts non-functional. The base package is set up to analyze data in the "acq4" format, but also has routines that translate from an older set of matlab and C-based formats specific to our lab.
The analysis part of the package is broken up into 4 parts: ephysanalysis, minianalysis, psc_analysis and mapanalysis, plus a set of tools that make use of these packages.
A GUI is available to help with the ephys analysis.
Requirements: Python3.11+, and modules specified in requirements_local.txt
This module provides tools for reading the lab data formats, for doing basic analysis of IV prototocols, spike shapes and rate adaptation, some voltage-clamp analyses (incomplete), and measures of EPSPs/EPSCs from particular protocols It also provides a routine (dataSummary) that generates tables from the header/index files of a directory of recordings, to aid in creating semi-automated analysis of datasets.
The MiniAnalysis class provides overall services that are commonly needed for both of the event detectors, including setups, making measurements of the events, fitting them, curating them, and plotting.
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Clements, J. D. & Bekkers, J. M. Detection of spontaneous synaptic events with an optimally scaled template. Biophys. J. 73, 220–229 (1997).
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Pernia-Andrade, A. J. et al. A deconvolution-based method with high sensitivity and temporal resolution for detection of spontaneous synaptic currents in vitro and in vivo. Biophys J 103, 1429–1439 (2012).
Clements Bekkers class can use a numba jit routine to speed things up (there is also a cython version floating around, but the numba one is easier to deal with). This is the classic sliding-template algorithm; it does not work well with overlapping events. The Pernia-Andrade et al. method uses numpy and scipy routines to implement a deconvolution approach; it works better with overlapping events. Two other algorithms are included (zero-crossing, Richardson-Silverberg), but have not been not fully tested.
There are some test routines that generate synthetic data, and which exercise the code.
The core code is in the mini_methods file, which provides a MiniAnalysis class and separate classes for each of the methods. A set of test routines (some of which currently fail because of changes in the underlying datasets) are included.
Usage:
mini_analysis.py (rarely called this way).
This module provides the MiniAnalysis class, which is a high-level wrapper that uses mini_methods_command and mini_methods to analyze events, organize the results, and create various summary plots of event distributions.
- Utilities
Several modules provide utilities. Best to inspect these; they are often special purpose.
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This is a small modulethat provides some tools for analysis of laser-scanning photostimulation maps.
getTable: a program that reads the datasummary table (see ephysanalysis), or can look for a protocol directory, displays the waveforms, and can use the Andreade-Jonas deconvolution algorithm to identify events. Events are marked on the traces. Also displayed are the average events, fits, and template, and a histogram of event times across all trials.
analyzeMapData: a program that is similar to getTable, without the GUI. Generates a matplotlib display of the map grid (color coded by amplitude), average waveforms, and the event histogram. It is designed to be called from a higher-level analysis program as well (that is current usage).
plotMapData is the routine that was used in the Zhang et al 2017 paper for the TTX plots (similar to analyzeMapData).
To read acq4 files (videos, scanning protocols, images): ephysanalysis (https://github.com/pbmanis/ephysanalysis) To analyze events, minis (provides Andrade-Jonas and Clements Bekkers): minis (https://github.com/pbmanis/mini_analysis) pylibrary (plotting, findspikes) (https://github.com/pbmanis/pylibrary)
pyqtgraph matplotlib seaborn xlrd pandas numpy re (regular expressions)
Usage: usage: analyzeMapData.py [-h] [-i] [-o DO_ONE] [-m DO_MAP] [-c] [-v] datadict
mini synaptic event analysis
positional arguments: datadict data dictionary
optional arguments: -h, --help show this help message and exit -i, --IV just do iv -o DO_ONE, --one DO_ONE just do one -m DO_MAP, --map DO_MAP just do one map -c, --check Check for files; no analysis -v, --view Turn off pdf for single run
A requirements file for doing a local install is provided, along with a bash shell script to create an environment.