Directory of repositories on this Github page. 
Computer code for analysing neurophysiological signals 🧠, including EEG and NIRS, recorded from infants in the neonatal intensive care unit. 👶 🏥
Also includes code for generic signal processing tools (such as time--frequency analysis) and machine learning tools.
Table of Contents
- Quantitative EEG (qEEG)
- Detecting Bursts or Inter-Bursts in Neonatal EEG
- Near Infraread Spectroscopy (NIRS)
- Heart Rate Variability (HRV)
- Tools for Time--Frequency Signal Analysis
- Tools for Connectivity
- Signal-Processing and Machine-learning Tools
- Code to Accompany Published Papers
- Plots for Review Paper on Time--Frequency Processing of Nonstationary Biomedical signals
- Monitoring cerebral oxygenation of preterm infants using a neonatal specific sensor
- Quantitative features of the EEG recorded minutes after birth
- Evolution of qEEG in preterm infants over the first days of life
- EEG concordance in preterm twins
- Curated set of quantitative features for neonatal EEG.
- Clearly defined features (full description and accompanying code).
- code: github (Matlab version)
- code: github @BrianMur92 (Python version)
- paper (preprint): arXiv:1704.05694
- Machine learning method to detect inter-burst intervals in preterm EEG.
- Developed and tested on a cohort of infants <30 weeks gestational age.
- code: github | Python version
- code: github | Matlab version
- paper: O'Toole et al., Med Eng Phys, 2017
- Generic method to detect bursts: high-amplitude coupled with high-frequency.
- Includes envelope derivative operator (EDO) and nonlinear energy operator (NLEO).
- code: github | Matlab version
- code: github | Python version
- paper: O'Toole et al., EMBC-2014
- Machine learning method to detect bursts and inter-bursts in term EEG during Quiet Sleep.
- Trained and tested on a cohort of healthy, normal newborns.
- code: github @sumitraurale | Matlab code
- paper: Raurale et al., EMBC-2020
- Method to detect short-duration bursts of activity in preterm (<30 weeks GA) EEG.
- code: github @BrianMur92 | Python code
- paper: Murphy et al., EMBC-2020
- Generates cerebral oxygenation-like signals (rcSO2).
- code: github | Matlab code
- papers: O'Toole et al., EMBC-2018 and Ashoori et al., EMBC-2021
- Method to extract sparse, transient-like signals from the cerebral oxygenation signals.
- Method is based on singular spectral analysis and signal rotation using the cosine transform.
- code: github | Matlab code
- paper: Ashoori et al., EMBC-2021
- Generates some standard features (e.g. spectral power ratios) of HRV.
- code: github | Matlab code
- papers (e.g.): Garvey et al., Pediatric Research, 2021
- Algorithms to compute quadratic TFDs.
- Saves computation and computer memory, thus enabling computation of TFDs for long-duration signals.
- code (recommend): github | Matlab code
- code (for exact TFD): github | Matlab code
- paper: O'Toole and Boashash, App Comp Harm Anal, 2013
- book chaper: JM O'Toole and B Boashash, “Memory Efficient Algorithms for Quadratic TFDs”, Chapter 6.6; in Time–Frequency Signal Processing and Analysis: A Comprenhensive Reference, Second Edition, Academic Press, pp. 374–385, 2016 (ISBN: 9780123984999).
- Two methods to extract/estimate the Instantaneous Frequency (IF) from TFDs.
- Method 1 uses an edge-linking strategy (see Rankine et al., 2007); Methods 2 uses the concept of finite duration IF components McAulay and Quatieri, 1986
- code: github | Matlab code
- papers: Rankine et al., 2007 and McAulay and Quatieri, 1986; also see list of references in github page.
- Code to generate a short-time information partial directed coherence (ST-iPDC) function and code to extract nonstationary and time-varying directional features from the ST-iPDC.
- Also includes a 2D fractal dimension measure.
- code: github | Matlab code
- paper: O'Toole et al., Physiological Measurement, 2021
- Zero-knowledge machine-learning algorithm.
- Adapted from ROCKET to incorporate multiscale analysis.
- code: github | Python code
- paper: Lundy and O'Toole, EUSIPCO-2021
- Fast implementation of methods for calculating mutual information, for both the continuous--continuous case and discrete--continuous case.
- code: github | Matlab code
- paper: Kraskov et al., 2004 and Ross 2014.
- A frequency-weighted energy operator (also used as burst-detector).
- code: github | Matlab version
- code: github | Python version
- paper: O'Toole et al., EMBC-2014
- Plot of time--frequency analysis methods in review paper for IEEE Signal Processing Magazine.
- code: github | Matlab code
- paper: Boashash et al., 2013
- Methods for determining association with short-term clinical outcome (brain injury or death) and cerebral oxygenation as measured by NIRS.
- code: github | R and Matlab code
- paper: DOI: 10.1038/s41372-017-0007-5
- Quantitative analysis of EEG recorded in the delivery room.
- code: github | Matlab code
- paper: DOI: 10.1136/archdischild-2018-315231
- Methods to track the evolution of the EEG over the first 3 days after birth.
- code: github | R and Matlab code
- paper: DOI: 10.1038/s41598-019-41227-9
- Methods to compare qEEG features between preterm singletons and twins.
- code: github | R and Matlab code
- paper: Lloyd et al., J Clin Neurphys, 2021
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