Mayo Sleep Spindles Research Project

Project Overview

This repository contains the implementation and research work related to sleep spindle detection and analysis conducted at Mayo Clinic. Sleep spindles are thalamocortical oscillations occurring during non-REM sleep that play crucial roles in memory consolidation, cognition, and neural development.

Graphical Abstract

Scalp and iEEG Data Visualization

Research Highlights

• Advanced detection of sleep spindles using neural network approaches
• Analysis of spindle characteristics across different patient populations
• Integration of scalp and intracranial EEG data for comprehensive spindle characterization

Installation Guide

On Linux and Windows the project can be used by running the following commands:

Using pip with virtualenv for Windows

# enter the project root
git clone https://github.com/yourusername/mayo_spindles.git
cd mayo_spindles
# Create the virtual env with pip
python -m venv venv
venv\Scripts\activate
pip install --upgrade pip
pip install -r requirements.txt
# With jupyter notebook
pip install ipykernel
pip install ipywidgets

Directory Structure

• mayo_spindles/: Core implementation of the project
• model_repo/: Repository of various models used in the project

OpenSpindleNet DREAMS Bundle Export

The TXT-only dreams-bundle used by openspindlenet eval is generated from this repository.

From the mayo_spindles repository root:

python mayo_spindles/create_dreams_repro_bundle.py --source_data DREAMS_HDF5 --bundle_dir ../openspindlenet/dreams-bundle --annotator_spec any

This exports DREAMS test split signals and labels as TXT files into openspindlenet/dreams-bundle/data and refreshes that folder's README.