ElectroPhysiology.jl

Overview

ElectroPhysiology.jl is the core data layer for electrophysiology workflows in Julia. It provides:

• File readers for ABF and two-photon image stacks
• A shared Experiment container (trial x time x channel)
• Stimulus protocol extraction and attachment
• Core trial/time/channel manipulation utilities
• ROI and image utility methods for two-photon data

Installation

Install from the Julia REPL:

using Pkg
Pkg.add("ElectroPhysiology")

Or in package mode:

pkg> add ElectroPhysiology

Quick Start

Read ABF data

using ElectroPhysiology

exp = readABF("example.abf"; stimulus_name = "IN 7")
println(size(exp))       # (n_trials, n_timepoints, n_channels)
println(getSampleFreq(exp))

Basic processing

exp2 = downsample(exp, 1000.0)
exp3 = truncate_data(exp2, 0.0, 1.0)
avg = average_trials(exp3)

Two-photon workflow

img = readImage("stack.tif")
deinterleave!(img, n_channels = 2)
pixel_splits_roi!(img, 16)
roi = getROIarr(img, 1)

Related Packages

This package is part of a larger ecosystem of physiology-related packages:

PhysiologyAnalysis.jl

A package for advanced analysis of physiological data. See documentation here

PhysiologyPlotting.jl

A package for creating publication-quality plots of physiological data. See documentation here

Documentation

• Package docs: mattar13.github.io/ElectroPhysiology.jl/dev
• API reference (source-aligned): docs/src/API.md

Development

Contributing

Contributions are welcome! Please feel free to submit a Pull Request. For major changes, please open an issue first to discuss what you would like to change.

Building Documentation

To build the documentation locally:

cd("docs")
using Pkg
Pkg.activate(".")
Pkg.instantiate()
include("make.jl")

License

This project is licensed under the MIT License - see the LICENSE file for details.