mne

Open-source Python package for exploring, visualizing, and analyzing human neurophysiological data including EEG, MEG, sEEG, and ECoG.

9 stars

Best use case

mne is best used when you need a repeatable AI agent workflow instead of a one-off prompt.

Open-source Python package for exploring, visualizing, and analyzing human neurophysiological data including EEG, MEG, sEEG, and ECoG.

Teams using mne should expect a more consistent output, faster repeated execution, less prompt rewriting.

When to use this skill

  • You want a reusable workflow that can be run more than once with consistent structure.

When not to use this skill

  • You only need a quick one-off answer and do not need a reusable workflow.
  • You cannot install or maintain the underlying files, dependencies, or repository context.

Installation

Claude Code / Cursor / Codex

$curl -o ~/.claude/skills/mne/SKILL.md --create-dirs "https://raw.githubusercontent.com/tondevrel/scientific-agent-skills/main/skills/mne/SKILL.md"

Manual Installation

  1. Download SKILL.md from GitHub
  2. Place it in .claude/skills/mne/SKILL.md inside your project
  3. Restart your AI agent — it will auto-discover the skill

How mne Compares

Feature / AgentmneStandard Approach
Platform SupportNot specifiedLimited / Varies
Context Awareness High Baseline
Installation ComplexityUnknownN/A

Frequently Asked Questions

What does this skill do?

Open-source Python package for exploring, visualizing, and analyzing human neurophysiological data including EEG, MEG, sEEG, and ECoG.

Where can I find the source code?

You can find the source code on GitHub using the link provided at the top of the page.

SKILL.md Source

# MNE - Neurophysiology Analysis

MNE provides sophisticated tools for filtering brain signals, epoching data, and performing source localization (mapping signals back to brain anatomy).

## When to Use

- Processing EEG/MEG recordings from clinical or research studies.
- Analyzing event-related potentials (ERPs).
- Source localization (finding where in the brain signals originate).
- Connectivity analysis between brain regions.
- Preprocessing neurophysiological data for machine learning.

## Core Principles

### Raw → Epochs → Evoked

The standard pipeline: continuous raw data → segmented epochs → averaged evoked responses.

### Sensor Space vs. Source Space

Sensor space: signals at electrodes. Source space: signals reconstructed at brain locations.

### Frequency Analysis

Brain signals are analyzed in frequency bands (delta, theta, alpha, beta, gamma).

## Quick Reference

### Standard Imports

```python
import mne
import numpy as np
```

### Basic Patterns

```python
# 1. Load data
raw = mne.io.read_raw_fif("sample_audvis_raw.fif")
# Or: raw = mne.io.read_raw_edf("eeg.edf")

# 2. Filter and cleaning
raw.filter(l_freq=1, h_freq=40)  # Bandpass filter
raw.notch_filter(freqs=[50, 100]) # Remove power line noise

# 3. Find events and create Epochs
events = mne.find_events(raw)
epochs = mne.Epochs(raw, events, event_id={'stimulus': 1}, tmin=-0.2, tmax=0.5)
epochs.average().plot() # Plot Evoked potential

# 4. Frequency analysis
epochs.compute_psd().plot()
```

## Critical Rules

### ✅ DO

- **Filter before epoching** - Apply filters to continuous data, not epochs.
- **Check data quality** - Use `raw.plot()` to visually inspect for artifacts.
- **Set montage** - Assign electrode positions for proper visualization.
- **Reject bad epochs** - Remove epochs with artifacts before averaging.

### ❌ DON'T

- **Don't filter too aggressively** - Over-filtering removes signal along with noise.
- **Don't ignore reference** - EEG signals are relative. Know your reference electrode.
- **Don't mix sampling rates** - Ensure all channels have the same sampling rate.

## Advanced Patterns

### Source Localization

```python
# Compute forward solution and inverse
fwd = mne.make_forward_solution(raw.info, trans, src, bem)
inv = mne.minimum_norm.make_inverse_operator(raw.info, fwd, cov)
stc = mne.minimum_norm.apply_inverse(evoked, inv)
stc.plot()
```

### Connectivity Analysis

```python
from mne.connectivity import spectral_connectivity

# Compute connectivity between channels
con, freqs, times, n_epochs, n_tapers = spectral_connectivity(
    epochs, method='coh', mode='multitaper')
```

MNE is the gold standard for neurophysiological data analysis, enabling researchers to extract meaningful insights from the complex signals of the human brain.

Related Skills

xgboost-lightgbm

9
from tondevrel/scientific-agent-skills

Industry-standard gradient boosting libraries for tabular data and structured datasets. XGBoost and LightGBM excel at classification and regression tasks on tables, CSVs, and databases. Use when working with tabular machine learning, gradient boosting trees, Kaggle competitions, feature importance analysis, hyperparameter tuning, or when you need state-of-the-art performance on structured data.

xarray

9
from tondevrel/scientific-agent-skills

N-dimensional labeled arrays and datasets in Python. Built on top of NumPy and Dask. It introduces labels in the form of dimensions, coordinates, and attributes on top of raw NumPy-like arrays, making data analysis in physical sciences more intuitive and less error-prone. Use for working with multi-dimensional scientific data, NetCDF/GRIB/Zarr files, climate/weather/oceanographic datasets, remote sensing, geospatial imaging, large out-of-memory datasets with Dask, and labeled array operations.

transformers

9
from tondevrel/scientific-agent-skills

State-of-the-art Machine Learning for PyTorch, TensorFlow, and JAX. Provides thousands of pretrained models to perform tasks on different modalities such as text, vision, and audio. The industry standard for Large Language Models (LLMs) and foundation models in science.

tqdm

9
from tondevrel/scientific-agent-skills

A fast, extensible progress bar for Python and CLI. Instantly makes your loops show a smart progress meter with ETA, iterations per second, and customizable statistics. Minimal overhead. Use for monitoring long-running loops, simulations, data processing, ML training, file downloads, I/O operations, command-line tools, pandas operations, parallel tasks, and nested progress bars.

tensorflow

9
from tondevrel/scientific-agent-skills

Comprehensive deep learning framework for building, training, and deploying neural networks. TensorFlow provides tf.keras high-level API for model construction, tf.data for efficient data pipelines, and tf.function for graph-mode optimization. Use when working with: neural network training and inference, image classification/detection/segmentation, NLP/text processing with embeddings or transformers, time series forecasting, generative models (VAE, GAN), transfer learning with pretrained models, custom training loops with GradientTape, GPU/TPU accelerated computation, or any deep learning task.

sympy

9
from tondevrel/scientific-agent-skills

Comprehensive guide for SymPy - Python library for symbolic mathematics. Use for symbolic expressions, calculus (derivatives, integrals, limits, series), equation solving (algebraic, differential, systems), linear algebra, simplification, matrix operations, special functions, code generation, and mathematical proofs. Essential for analytical mathematics and computer algebra.

sunpy

9
from tondevrel/scientific-agent-skills

The community-developed free and open-source software package for solar physics. Provides tools for data search and download, coordinate transformations specific to solar physics, and powerful image processing through the Map object. Use when working with solar data, solar images (EUV, magnetograms, white light), solar coordinates (Helioprojective, Heliographic), Fido data search, solar time series, differential rotation, limb fitting, or multi-instrument solar analysis (AIA, HMI, GOES).

statsmodels

9
from tondevrel/scientific-agent-skills

Advanced statistical modeling and hypothesis testing. Complementary to SciPy's stats module, it provides classes and functions for the estimation of many different statistical models, as well as for conducting statistical tests and statistical data exploration. Use for linear regression, GLM, time series analysis, ANOVA, survival analysis, causal inference, and statistical hypothesis testing. Load when working with OLS, WLS, logistic regression, Poisson regression, ARIMA, SARIMAX, statistical diagnostics, p-values, confidence intervals, or R-style statistical analysis.

spacy-nltk

9
from tondevrel/scientific-agent-skills

Natural Language Processing for text analysis, corpus linguistics, and production NLP pipelines. spaCy provides fast production-grade tokenization, POS tagging, NER, dependency parsing, and custom model training. NLTK provides classical corpus linguistics, linguistic analysis, VADER sentiment, collocation analysis, and access to standard linguistic corpora. Use when: processing and analyzing text data, extracting named entities (people, orgs, locations, dates), dependency parsing and syntactic analysis, building text classification pipelines, performing corpus-level linguistic analysis (frequency, collocations, readability), sentiment analysis, lemmatization and stemming, working with multilingual text, training custom NER or text classifiers, or any task requiring structured understanding of natural language beyond simple string operations.

sktime-tsfresh

9
from tondevrel/scientific-agent-skills

Time series machine learning layer (Tier 1): integration of **sktime** and **tsfresh** for building production-grade pipelines that transform raw time series into tabular feature representations suitable for classical machine-learning models. *sktime* provides a unified, sklearn-compatible interface for time-series data types, transformations, and pipelines, while *tsfresh* enables large-scale automated extraction of statistical, spectral, and autocorrelation features, with optional statistically grounded feature relevance selection (FRESH).

sklearn-explainability

9
from tondevrel/scientific-agent-skills

Advanced sub-skill for scikit-learn focused on model interpretability, feature importance, and diagnostic tools. Covers global and local explanations using built-in inspection tools and SHAP/LIME integrations.

sklearn-advanced

9
from tondevrel/scientific-agent-skills

Professional sub-skill for scikit-learn focused on robust pipeline architecture, custom estimator development, advanced feature engineering, and rigorous model validation. Covers Target Encoding, Nested Cross-Validation, and Production Deployment.