Select Page

Research digital skills training 2021

The Coronary Atlas – data processing workflow optimisation

Ryan Huynh, Sina Masoud-Ansari, Centre for eResearch; Dr Susann Beier, principal investigator of the project, was the research fellow of the University of Auckland; currently a Lecturer at the University of New South Wales.

Home • Projects • The Coronary Atlas – data processing workflow optimisation
The image is credited to https://www.coronaryatlas.org/

The coronary atlas project aims to understand individual differences in the blood flow environment to generate insights into disease susceptibility for prevention and treatment improvement. The team consists of multiple disciplinary domains including cardiology, medical imaging, fluid dynamics and aerodynamics, computer science, biology, anatomical and statistical model and machine learning experts, Auckland City Hospital and Auckland Heart Group. Note: Dr Susann Beier, principal investigator of the project, was the research fellow of the University of Auckland; currently a Lecturer at the University of New South Wales.

Introduction

“Describing the detailed statistical anatomy of the coronary artery tree is important for determining the aetiology of heart disease. A number of studies have investigated geometrical features and have found that these correlate with clinical outcomes, e.g. bifurcation angle with major adverse cardiac events. These methodologies were mainly two-dimensional, manual and prone to inter-observer variability, and the data commonly relates to cases already with pathology. We propose a hybrid atlasing methodology to build a population of computational models of the coronary arteries to comprehensively and accurately assess anatomy including 3D size, geometry and shape descriptors. A random sample of 120 cardiac 64-CT 3D scans with a calcium score of zero was segmented and analysed using a standardised protocol. The resulting atlas includes, but is not limited to, the distributions of the coronary tree in terms of angles, diameters, centrelines, principal component shape analysis and cross-sectional contours. This novel resource will facilitate the improvement of stent design and provide a reference for hemodynamic simulations, and provides a basis for large normal and pathological database.1

The role of the Centre for eResearch

As part of the research, the Centre for eResearch specialist developed multiple machine learning algorithms and Python scripts to fully automate various workflows in data cleansing, anatomical analyses on 3D models, anomaly detection and segmentation on computed tomographic coronary angiographic (CTCA) images. In addition, we also modelled and streamlined the data management process in order to improve the data quality in the project’s machine learning pipeline.

Coronary artery segmentation using deep learning

Coronary artery lumen segmentation is an important but challenging task given the nature of noise in CTCA images. Deep learning, specifically 3D U-net convolutional neural networks2 (Figure 1) has been very successful in volumetric segmentation for medical imaging.

 

 

Previously, the work on semi-automated segmentation by using software MiaLite was performed by research assistants. However, The Centre for eResearch assisted Susann to develop and implement a fully automated workflow, which also generated more accurate predictions. We built a system of two deep learning neural networks. Each network follows the U-net CNN architecture and contains 22 layers of 3D convolution, max pooling, batch normalisations and 3D up sampling. The first network was trained on augmented input images in high resolution patches to select voxels that may belong to coronary artery. The second was trained on normal resolution patches to detect the location of the two main coronary arteries. The post-processing algorithm then chooses the intersected branches between the outputs of these networks. As a result, our deep learning models achieved a mean Dice similarity coefficient (DSC) of 0.819, which was higher than the previous method with a mean DSC of 0.096 and the baseline U-Net model with a mean DSC of 0.591. Our framework also performed a complete, robust segmentation of the coronary arteries given the benefits of data augmentation implementation in our neural network.
Figure 1.U-net architectur2

Automated anomaly detection for medical images

CTCA scan images often contain texts3 that are not useful for analysis purposes (Figure 2). We implemented an unsupervised density-based spatial of clustering of applications with noise (DBASCAN) algorithm to detect these anomalies. The algorithm takes the mean and standard deviation of pixel values of each slice throughout the volumetric CTCA scans and filters out the anomalies. As a result, we ensured the high quality of input data to our machine learning models. Our framework could also be applied widely in medical imaging and other area.

Figure 2. An example of CT image with texts 3

Anatomical assessment of coronary arteries

A random sample of more than 1200 cardiac 64-CT 3D scans was segmented and analysed using a standardised protocol. We applied advanced quantitative models to assess the anatomy of a arteries. The resulting atlas includes the distributions of the coronary tree in terms of angles (figure 3)4, diameters and centrelines.

Figure 3. Spatial characteristics of coronary bifurcation4

Streamline data management processes

For a typical biomedical project, the data management processes involve many different stakeholders such as nurses, radiologists, IT technicians and researchers at universities. To streamline these complex processes, we modelled the protocols using data flow charts (DFCs) to document every angle of the data pipeline. After that, we removed any redundancy plus risks to ensure efficiency and quality of the data. We suggested changes and new tools that further streamlined the processes. As a result, we shortened process timeline by over 50%, in addition to an increase in quality of the data.

Reference

  1. Pau Medrano-Gracia; John Ormiston, Mark Webster, Susann Beier, Chris Ellis, Chunliang Wang, Alistair A. Young, Brett R. Cowan; “ Construction of a Coronary Arterey Atlas from CT Angiography” , International Conference on Medical Image Computing and Computer-Assisted Intervention
  2. Olaf RonnebergerPhilipp FischerThomas Brox; “U-Net: Convolutional Networks for Biomedical Image Segmentation”
  3. Emre Ünal, Musturay Karcaaltincaba, Erhan Akpinar, Orhan Macit Ariyurek; “The imaging appearances of various pericardial disorders”
  4. Yang Yang, Xin Liu, Yufa Xia, Xin Liu, Wanqing Wu, Huahua Xiong, Heye Zhang, Lin Xu, Kelvin K. L. Wong, Hanbin Ouyang, Wenhua Huang; “Impact of spatial characteristics in the left stenotic coronary artery on the hemodynamics and visualization of 3D replica models”

See more case study projects

Data maturity project in High Value Nutrition, National Science Challenge

Data maturity project in High Value Nutrition, National Science Challenge

Haka on the move: sport circuits and cultural performance 

Haka on the move: sport circuits and cultural performance 

Proteins under a computational microscope: designing in-silico strategies to understand and develop molecular functionalities in Life Sciences and Engineering

Proteins under a computational microscope: designing in-silico strategies to understand and develop molecular functionalities in Life Sciences and Engineering

Remote temperature monitoring to reduce the spread of COVID-19

Remote temperature monitoring to reduce the spread of COVID-19

COVID-19 exponential growth visualisation

COVID-19 exponential growth visualisation

Developing virtual capabilities for the Science Payload Operations Centre

Developing virtual capabilities for the Science Payload Operations Centre

Hosting visualisation and analytics tools for COVID-19 studies

Hosting visualisation and analytics tools for COVID-19 studies

Exploring perceptions towards climate change over time on Twitter

Exploring perceptions towards climate change over time on Twitter

Coastal image classification and nalysis based on convolutional neural betworks and pattern recognition

Coastal image classification and nalysis based on convolutional neural betworks and pattern recognition

Calcium signalling in salivary gland acinar cells

Calcium signalling in salivary gland acinar cells

Anti-corruption regulations for promoting socially responsible practices

Anti-corruption regulations for promoting socially responsible practices

Determinants of translation efficiency in the evolutionarily-divergent protist Trichomonas vaginalis

Determinants of translation efficiency in the evolutionarily-divergent protist Trichomonas vaginalis

Analysing text data by time-series feature engineering

Analysing text data by time-series feature engineering

An investigation into Leap Motion device for “gesture-as-sign”

An investigation into Leap Motion device for “gesture-as-sign”

Antibiotic resistance and the “end of modern medicine ”

Antibiotic resistance and the “end of modern medicine ”

Develop short-term eruption warning systems for Whakaari and other volcanoes

Develop short-term eruption warning systems for Whakaari and other volcanoes

Evenly spaced observation fields from irregularly sampled data in the Southern Ocean

Evenly spaced observation fields from irregularly sampled data in the Southern Ocean

Measuring impact of entrepreneurship activities on students’ mindset, capabilities and entrepreneurial intentions

Measuring impact of entrepreneurship activities on students’ mindset, capabilities and entrepreneurial intentions

Using Zebra Finch data and deep learning classification to identify individual bird calls from audio recordings

Using Zebra Finch data and deep learning classification to identify individual bird calls from audio recordings

NETwork! analysis in cancer – managing genomics research data and building a repository workflow

NETwork! analysis in cancer – managing genomics research data and building a repository workflow

The Coronary Atlas – data processing workflow optimisation

The Coronary Atlas – data processing workflow optimisation

3D visualisation of indigenous burial site in Roonka

3D visualisation of indigenous burial site in Roonka

Automated measurement of intracranial cerebrospinal fluid volume and outcome after endovascular thrombectomy for ischemic stroke

Automated measurement of intracranial cerebrospinal fluid volume and outcome after endovascular thrombectomy for ischemic stroke

A new ‘stratigraphy’: interpreting object relationships with 3D point densities

A new ‘stratigraphy’: interpreting object relationships with 3D point densities

Towards the use of deep learning techniques for storm surge prediction

Towards the use of deep learning techniques for storm surge prediction

Using simple models to explore complex dynamics: A case study of macomona liliana (wedge-shell) and nutrient variations

Using simple models to explore complex dynamics: A case study of macomona liliana (wedge-shell) and nutrient variations

Development of Machine Learning methodology for genomic research

Development of Machine Learning methodology for genomic research

An Archaeological database for threatened North Island rock art in New Zealand

An Archaeological database for threatened North Island rock art in New Zealand

Presence: distributed mixed reality learning environment

Presence: distributed mixed reality learning environment

Digital video and the early learning lab

Digital video and the early learning lab

Publishing the Bay of Island Bottlenose dolphin catalogue

Publishing the Bay of Island Bottlenose dolphin catalogue

Modelling the diurnal cycle* of winds and clouds

Modelling the diurnal cycle* of winds and clouds

Presence: distributed mixed reality learning environment

Presence: distributed mixed reality learning environment

Using research virtual machines to analyse fMRI datasets

Using research virtual machines to analyse fMRI datasets

Genomic Virtual Lab (GVL) as a bioinformatics training platform

Genomic Virtual Lab (GVL) as a bioinformatics training platform

SwiftLaTeX- Exploring web-based true WYSIWYG editing for digital publishing

SwiftLaTeX- Exploring web-based true WYSIWYG editing for digital publishing

Climate change impacts on weather-related hazards

Climate change impacts on weather-related hazards

Understanding tumour evolution through augmented reality

Understanding tumour evolution through augmented reality

Myocardial motion tracking and strain calculation using Deep Learning networks

Myocardial motion tracking and strain calculation using Deep Learning networks

OnTask pilot at the Centre for Learning and Research in Higher Education

OnTask pilot at the Centre for Learning and Research in Higher Education

Visualising the University campus in 3D

Visualising the University campus in 3D

Visualising protein interaction

Visualising protein interaction

Biological heritage National Science Challenge eDNA virtual hub

Biological heritage National Science Challenge eDNA virtual hub

Interactive AR art – Project Gordon

Interactive AR art – Project Gordon

1-D numerical models of post-glacial river evolution

1-D numerical models of post-glacial river evolution

Mathematically modelling gastrointestinal electrical activity

Mathematically modelling gastrointestinal electrical activity

3D Cryo-EM reconstructions of macromolecular complexes

3D Cryo-EM reconstructions of macromolecular complexes

Engine knock in a spark-ignition engine with hydrogen supplementation

Engine knock in a spark-ignition engine with hydrogen supplementation

The complex unsteady flow within a fluid-filled annulus and its transition to turbulence

The complex unsteady flow within a fluid-filled annulus and its transition to turbulence

Using data mining for digital ink recognition

Using data mining for digital ink recognition

The landscape costs of brushtail possum dispersal

The landscape costs of brushtail possum dispersal

Accelerating the discovery of natural products made by orphan megasynthases

Accelerating the discovery of natural products made by orphan megasynthases

Improving the short term precipitation forecasts for New Zealand

Improving the short term precipitation forecasts for New Zealand

Finding genetic variants responsible  for human disease hiding in the universe of benign variants

Finding genetic variants responsible for human disease hiding in the universe of benign variants

Revealing key processes in enzyme efficiency through high performance computing

Revealing key processes in enzyme efficiency through high performance computing

3D Electromagnetic modeling and simulation using heterogeneous computing

3D Electromagnetic modeling and simulation using heterogeneous computing

Hemodynamics in the microcirculation

Hemodynamics in the microcirculation

Putting turbulence to work

Putting turbulence to work

Why are some molecules drugs?

Why are some molecules drugs?

Bayesian additive regression trees  vs logistic regression – estimation of propensity scores

Bayesian additive regression trees vs logistic regression – estimation of propensity scores

Fully coupled thermo-hydro-mechanical modelling of permeability enhancement by the finite element method

Fully coupled thermo-hydro-mechanical modelling of permeability enhancement by the finite element method

Modelling dispersal and ecological competition in a statistical phylogeographic framework

Modelling dispersal and ecological competition in a statistical phylogeographic framework

Studying the shape and the size of the universe

Studying the shape and the size of the universe

Planet hunting

Planet hunting

Simulating quantum mechanics on high performance computing cluster

Simulating quantum mechanics on high performance computing cluster

Multiscale modelling of saliva secretion

Multiscale modelling of saliva secretion

Modelling dual reflux pressure swing adsorption (DR-PSA) units for gas separation in natural gas processing

Modelling dual reflux pressure swing adsorption (DR-PSA) units for gas separation in natural gas processing

Improving the treatment of heart disease

Improving the treatment of heart disease

Estimating migration rates in the budding yeast Saccharomyces cerevisiae

Estimating migration rates in the budding yeast Saccharomyces cerevisiae

Number theoretic algorithms in cryptography

Number theoretic algorithms in cryptography

Molecular phylogenetics uses genetic data to reconstruct the evolutionary history of individuals, populations or species

Molecular phylogenetics uses genetic data to reconstruct the evolutionary history of individuals, populations or species

Phylogeny and phylogeography of the family kyphosidae (Perciformes: teleostei)

Phylogeny and phylogeography of the family kyphosidae (Perciformes: teleostei)

Testing what cosmic inflation really predicts

Testing what cosmic inflation really predicts

Multigene environmental DNA data analysis for New Zealand genomic observatory

Multigene environmental DNA data analysis for New Zealand genomic observatory

Finding genetic variants responsible for human disease hiding in universe of benign variants

Finding genetic variants responsible for human disease hiding in universe of benign variants

BEAST, Bayesian evolutionary analysis sampling trees

BEAST, Bayesian evolutionary analysis sampling trees

The formation of surface archaeological deposits in arid Australia

The formation of surface archaeological deposits in arid Australia

Statistical modelling of carryover effects after cessation of treatments

Statistical modelling of carryover effects after cessation of treatments

High-resolution cryo-electron microscopy of protein complexes and machines

High-resolution cryo-electron microscopy of protein complexes and machines

ARCI, archaeology eResearch collaboration initiative

ARCI, archaeology eResearch collaboration initiative

Optimisation of blades on large wind turbines with individual pitch control and trailing edge flaps

Optimisation of blades on large wind turbines with individual pitch control and trailing edge flaps

Quality of care and outcomes in children with cleft lip and/or palate

Quality of care and outcomes in children with cleft lip and/or palate

Geographic and temporal information retrieval on massive document collections

Geographic and temporal information retrieval on massive document collections

Homodynamics in the microcirculation

Homodynamics in the microcirculation

Processing structure-from-motion photogrammetry on the cluster

Processing structure-from-motion photogrammetry on the cluster

Computational investigation of catalysis mechanisms for polyurethane synthesis

Computational investigation of catalysis mechanisms for polyurethane synthesis

Virtual childhood obesity prevention laboratory

Virtual childhood obesity prevention laboratory

Giving Pacific research greater reach

Giving Pacific research greater reach

Development of novel waveguides  in the terahertz (THz) region

Development of novel waveguides in the terahertz (THz) region

Modelling of costs of diets  by INFORMAS

Modelling of costs of diets by INFORMAS

Foodback

Foodback

Finite element method code for  modelling biological cells

Finite element method code for modelling biological cells

The future of memory: Neuroimaging memory and imagination with functional MRI

The future of memory: Neuroimaging memory and imagination with functional MRI

Modelling and visualisation of calcium waves in parotid acinar cells

Modelling and visualisation of calcium waves in parotid acinar cells

Mapping donor contributions in the Pacific

Mapping donor contributions in the Pacific

Visualising humpback whale migration

Visualising humpback whale migration

Visualising the 2010 and 2011  Canterbury earthquakes

Visualising the 2010 and 2011 Canterbury earthquakes

Data management planning for MOA*

Data management planning for MOA*

Research data publishing  and preservation at COMPASS

Research data publishing and preservation at COMPASS

Centre for eResearch machine learning service

Centre for eResearch machine learning service

Building a discrete global  grid gazetteer service

Building a discrete global grid gazetteer service

The new Wanhal catalogue

The new Wanhal catalogue

Passive acoustic modelling

Passive acoustic modelling

Using GPUs to expand our understanding of the Solar System

Using GPUs to expand our understanding of the Solar System

Shedding new light on dark matter

Shedding new light on dark matter

Aerodynamics modelling paves the way for improved yacht designs

Aerodynamics modelling paves the way for improved yacht designs

Modernising models to help diagnose or treat disease and injury

Modernising models to help diagnose or treat disease and injury

Wandering around the molecular landscape: embracing virtual reality as a research showcasing outreach and teaching tool

Wandering around the molecular landscape: embracing virtual reality as a research showcasing outreach and teaching tool

ALTER: Between human and nonhuman – a VR art exhibition

ALTER: Between human and nonhuman – a VR art exhibition

Disposition of Microsoft HoloLenses for a Pop-Up Reality Shop to demonstrate the progress of a research project

Disposition of Microsoft HoloLenses for a Pop-Up Reality Shop to demonstrate the progress of a research project

Improving diagnosis for schistosomiasis by using the ‘metabolic footprint’ of urine samples from an animal model of Schistosoma infection to identify possible biomarkers

Improving diagnosis for schistosomiasis by using the ‘metabolic footprint’ of urine samples from an animal model of Schistosoma infection to identify possible biomarkers

Making stroke recovery prediction tools freely available

Making stroke recovery prediction tools freely available

MFT-ICR mass spectrometry data management and analysis workflow

MFT-ICR mass spectrometry data management and analysis workflow

Taking a ‘Big Data’ approach to find new clinical-omic associations in cancer

Taking a ‘Big Data’ approach to find new clinical-omic associations in cancer

Growing Up in New Zealand

Growing Up in New Zealand

Improving arrival time predictions for vehicles in a public transport network

Improving arrival time predictions for vehicles in a public transport network

Distributed and cloud-based control at field-level for systems interacting with soft bodies

Distributed and cloud-based control at field-level for systems interacting with soft bodies

Mobile Click Fraud Attack (MCFA)

Mobile Click Fraud Attack (MCFA)

Skin-omics: exploring the volatile organic compounds on human skin

Skin-omics: exploring the volatile organic compounds on human skin

New analytics tools for workload planning for the 2018 New Zealand Census

New analytics tools for workload planning for the 2018 New Zealand Census

Visualising the New Zealand Index of Multiple Deprivation

Visualising the New Zealand Index of Multiple Deprivation