MUedit

Decomposes high-density EMG signals into motor unit pulse trains.

Status

This software is functional and ready for use. The adapt_decomp feature still requires fine tuning and remains in beta. We continue to actively maintain and update these tools in line with the advancements of our research projects, and we welcome any contributions to make them useful for the wider community.

Features

• High-density EMG decomposition into motor unit pulse trains
• Adaptive decomposition workflows (via adapt_decomp)
• Web-based interface with FastAPI backend and JavaScript frontend
• Cross-platform launchers (macOS/Linux and Windows)
• Interactive editing of decomposed motor units
• BIDS-compliant export of raw EMG and decomposition results

Supported Input Formats

Format	Extension	Description
MATLAB	.mat	v5 and v7.3 (HDF5) signal structs
OTB+	.otb+	OT Biolab+ archive (tar/zip with XML + .sig)
OTB4	.otb4	OT Biolab4 proprietary binary format
BIDS EMG	.bdf, .edf	BIDS-formatted recordings with a _channels.tsv sidecar (legacy _emg_channels.tsv also accepted)
Decomposition	.npz	Saved decomposition output (for editing)

For BIDS input, point to either the *_emg.bdf/.edf file directly. The loader reads all grids and auxiliary channels defined in the accompanying *_channels.tsv.

Requirements

• Python 3.11+
• Conda (Anaconda or Miniconda)

Quick Start

1. Create and activate the conda environment:

conda env create -f environment.yml
conda activate MUedit

2. Install MUedit in editable mode:

pip install -e .

3. Launch the app from the repository root:

macOS / Linux:

./scripts/run_MUedit.sh

Windows (PowerShell):

.\scripts\run_MUedit.ps1

The launcher starts:

• Backend API on http://localhost:8000
• Frontend on http://localhost:8080

The browser opens automatically unless disabled via env var.

Windows first-time setup (if script execution is blocked):

Set-ExecutionPolicy -Scope CurrentUser RemoteSigned

CLI Entrypoints

After installation, MUedit exposes:

• muedit-api — starts the FastAPI backend
• muedit-decompose — runs decomposition from the terminal

Verify Installation

With MUedit running:

1. Open http://localhost:8080 in a browser.
2. Check backend health:

curl http://localhost:8000/api/v1/health

Troubleshooting

• python: command not found — activate the conda env before launching.
• Port already in use — set MUEDIT_BACKEND_PORT / MUEDIT_FRONTEND_PORT to free ports.
• Browser does not open automatically — open http://localhost:8080 manually.

Documentation

• User guide: docs/user-guide.md
• Saved files reference: docs/saved-files.md
• Loader registry guide: docs/loader-registry.md

Acknowledgment

This project includes code from adapt_decomp (see python/src/adapt_decomp) for adaptive decomposition workflows. Original author: Irene Mendez Guerra Original repository: https://github.com/imendezguerra/adapt_decomp