1,472 research outputs found
Automated Distinct Bone Segmentation from Computed Tomography Images using Deep Learning
Large-scale CT scans are frequently performed for forensic and diagnostic purposes, to plan and
direct surgical procedures, and to track the development of bone-related diseases. This often
involves radiologists who have to annotate bones manually or in a semi-automatic way, which is
a time consuming task. Their annotation workload can be reduced by automated segmentation
and detection of individual bones. This automation of distinct bone segmentation not only has
the potential to accelerate current workflows but also opens up new possibilities for processing
and presenting medical data for planning, navigation, and education.
In this thesis, we explored the use of deep learning for automating the segmentation of all
individual bones within an upper-body CT scan. To do so, we had to find a network architec-
ture that provides a good trade-off between the problem’s high computational demands and the
results’ accuracy. After finding a baseline method and having enlarged the dataset, we set out
to eliminate the most prevalent types of error. To do so, we introduced an novel method called
binary-prediction-enhanced multi-class (BEM) inference, separating the task into two: Distin-
guishing bone from non-bone is conducted separately from identifying the individual bones.
Both predictions are then merged, which leads to superior results. Another type of error is tack-
led by our developed architecture, the Sneaky-Net, which receives additional inputs with larger
fields of view but at a smaller resolution. We can thus sneak more extensive areas of the input
into the network while keeping the growth of additional pixels in check.
Overall, we present a deep-learning-based method that reliably segments most of the over
one hundred distinct bones present in upper-body CT scans in an end-to-end trained matter
quickly enough to be used in interactive software. Our algorithm has been included in our
groups virtual reality medical image visualisation software SpectoVR with the plan to be used
as one of the puzzle piece in surgical planning and navigation, as well as in the education of
future doctors
2023-2024 Catalog
The 2023-2024 Governors State University Undergraduate and Graduate Catalog is a comprehensive listing of current information regarding:Degree RequirementsCourse OfferingsUndergraduate and Graduate Rules and Regulation
Towards a muon collider
A muon collider would enable the big jump ahead in energy reach that is needed for a fruitful exploration of fundamental interactions. The challenges of producing muon collisions at high luminosity and 10 TeV centre of mass energy are being investigated by the recently-formed International Muon Collider Collaboration. This Review summarises the status and the recent advances on muon colliders design, physics and detector studies. The aim is to provide a global perspective of the field and to outline directions for future work
The 2023 wearable photoplethysmography roadmap
Photoplethysmography is a key sensing technology which is used in wearable devices such as smartwatches and fitness trackers. Currently, photoplethysmography sensors are used to monitor physiological parameters including heart rate and heart rhythm, and to track activities like sleep and exercise. Yet, wearable photoplethysmography has potential to provide much more information on health and wellbeing, which could inform clinical decision making. This Roadmap outlines directions for research and development to realise the full potential of wearable photoplethysmography. Experts discuss key topics within the areas of sensor design, signal processing, clinical applications, and research directions. Their perspectives provide valuable guidance to researchers developing wearable photoplethysmography technology
Introduction to Facial Micro Expressions Analysis Using Color and Depth Images: A Matlab Coding Approach (Second Edition, 2023)
The book attempts to introduce a gentle introduction to the field of Facial
Micro Expressions Recognition (FMER) using Color and Depth images, with the aid
of MATLAB programming environment. FMER is a subset of image processing and it
is a multidisciplinary topic to analysis. So, it requires familiarity with
other topics of Artifactual Intelligence (AI) such as machine learning, digital
image processing, psychology and more. So, it is a great opportunity to write a
book which covers all of these topics for beginner to professional readers in
the field of AI and even without having background of AI. Our goal is to
provide a standalone introduction in the field of MFER analysis in the form of
theorical descriptions for readers with no background in image processing with
reproducible Matlab practical examples. Also, we describe any basic definitions
for FMER analysis and MATLAB library which is used in the text, that helps
final reader to apply the experiments in the real-world applications. We
believe that this book is suitable for students, researchers, and professionals
alike, who need to develop practical skills, along with a basic understanding
of the field. We expect that, after reading this book, the reader feels
comfortable with different key stages such as color and depth image processing,
color and depth image representation, classification, machine learning, facial
micro-expressions recognition, feature extraction and dimensionality reduction.
The book attempts to introduce a gentle introduction to the field of Facial
Micro Expressions Recognition (FMER) using Color and Depth images, with the aid
of MATLAB programming environment.Comment: This is the second edition of the boo
A review of technical factors to consider when designing neural networks for semantic segmentation of Earth Observation imagery
Semantic segmentation (classification) of Earth Observation imagery is a
crucial task in remote sensing. This paper presents a comprehensive review of
technical factors to consider when designing neural networks for this purpose.
The review focuses on Convolutional Neural Networks (CNNs), Recurrent Neural
Networks (RNNs), Generative Adversarial Networks (GANs), and transformer
models, discussing prominent design patterns for these ANN families and their
implications for semantic segmentation. Common pre-processing techniques for
ensuring optimal data preparation are also covered. These include methods for
image normalization and chipping, as well as strategies for addressing data
imbalance in training samples, and techniques for overcoming limited data,
including augmentation techniques, transfer learning, and domain adaptation. By
encompassing both the technical aspects of neural network design and the
data-related considerations, this review provides researchers and practitioners
with a comprehensive and up-to-date understanding of the factors involved in
designing effective neural networks for semantic segmentation of Earth
Observation imagery.Comment: 145 pages with 32 figure
Semi-automated learning strategies for large-scale segmentation of histology and other big bioimaging stacks and volumes
Labelled high-resolution datasets are becoming increasingly common and necessary in different areas of biomedical imaging. Examples include: serial histology and ex-vivo MRI for atlas building, OCT for studying the human brain, and micro X-ray for tissue engineering. Labelling such datasets, typically, requires manual delineation of a very detailed set of regions of interest on a large number of sections or slices. This process is tedious, time-consuming, not reproducible and rather inefficient due to the high similarity of adjacent sections.
In this thesis, I explore the potential of a semi-automated slice level segmentation framework and a suggestive region level framework which aim to speed up the segmentation process of big bioimaging datasets. The thesis includes two well validated, published, and widely used novel methods and one algorithm which did not yield an improvement compared to the current state-of the-art.
The slice-wise method, SmartInterpol, consists of a probabilistic model for semi-automated segmentation of stacks of 2D images, in which the user manually labels a sparse set of sections (e.g., one every n sections), and lets the algorithm complete the segmentation for other sections automatically. The proposed model integrates in a principled manner two families of segmentation techniques that have been very successful in brain imaging: multi-atlas segmentation and convolutional neural networks.
Labelling every structure on a sparse set of slices is not necessarily optimal, therefore I also introduce a region level active learning framework which requires the labeller to annotate one region of interest on one slice at the time. The framework exploits partial annotations, weak supervision, and realistic estimates of class and section-specific annotation effort in order to greatly reduce the time it takes to produce accurate segmentations for large histological datasets.
Although both frameworks have been created targeting histological datasets, they have been successfully applied to other big bioimaging datasets, reducing labelling effort by up to 60−70% without compromising accuracy
Production and characterisation of dipolar Bose–Einstein condensates
Remarkable progress in the field of ultracold atoms has enabled the study of a great variety of topics in many-body quantum mechanics. The precise control of key parameters, such as interactions, temperature, density, internal and external degrees of freedom, dimensionality and the trapping geometry makes them a powerful and flexible experimental platform.
The ability to create degenerate samples of atoms which feature long-range and anisotropic dipole–dipole interactions besides the more conventional short-range and isotropic contact interactions drew considerable attention, enabling the creation of quantum droplets and a supersolid phase. This thesis reports on experimental and theoretical progress in investigating dipolar many-body quantum systems. We present an overview of our experimental apparatus and the techniques used for obtaining a Bose–Einstein condensate (BEC) of erbium. We then discuss our experimental sequence for producing a quantum degenerate gas, creating a quasi-pure BEC with 2.2 x 10^5 atoms. To optimise the production of erbium BECs, we explore density- and temperature-dependent losses in 166Er and identify six previously unreported resonant loss features. Finally, to enable studies of density-dependent phenomena, we present a theoretical investigation of dipolar condensates in box-like traps, where we explore stability and how one can use it to replicate properties of an infinite, homogeneous system to study dipolar physics. We found that traps with hard walls trigger roton-like density oscillations even if the bulk of the system is far from the roton regime, so smoother potentials are better suited to recreate homogeneous conditions. This sets the ground for future experiments, where the atoms will be loaded into a box trap to enable studies of systems which are tightly trapped in one direction but homogeneous in the other two
Artificial Intelligence for the Edge Computing Paradigm.
With modern technologies moving towards the internet of things where seemingly every financial, private, commercial and medical transaction being carried out by portable and intelligent devices; Machine Learning has found its way into every smart device and application possible. However, Machine Learning cannot be used on the edge directly due to the limited capabilities of small and battery-powered modules. Therefore, this thesis aims to provide light-weight automated Machine Learning models which are applied on a standard edge device, the Raspberry Pi, where one framework aims to limit parameter tuning while automating feature extraction and a second which can perform Machine Learning classification on the edge traditionally, and can be used additionally for image-based explainable Artificial Intelligence. Also, a commercial Artificial Intelligence software have been ported to work in a client/server setups on the Raspberry Pi board where it was incorporated in all of the Machine Learning frameworks which will be presented in this thesis. This dissertation also introduces multiple algorithms that can convert images into Time-series for classification and explainability but also introduces novel Time-series feature extraction algorithms that are applied to biomedical data while introducing the concept of the Activation Engine, which is a post-processing block that tunes Neural Networks without the need of particular experience in Machine Leaning. Also, a tree-based method for multiclass classification has been introduced which outperforms the One-to-Many approach while being less complex that the One-to-One method.\par
The results presented in this thesis exhibit high accuracy when compared with the literature, while remaining efficient in terms of power consumption and the time of inference. Additionally the concepts, methods or algorithms that were introduced are particularly novel technically, where they include:
• Feature extraction of professionally annotated, and poorly annotated time-series.
• The introduction of the Activation Engine post-processing block.
• A model for global image explainability with inference on the edge.
• A tree-based algorithm for multiclass classification
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Taking shape: The data science of elastic shape analysis with practical applications
This thesis was submitted for the award of Doctor of Philosophy and was awarded by Brunel University London.A mathematical curve can represent many different objects, both physical and abstract,
from the outline curve of an artefact in an image to the weight of growing animal to
the set of frequencies used in a sound. Regardless of these variations, the curves can
almost always vary non-linearly. One way to study shapes and their potential variations
is elastic shape analysis, a rich theory of which has developed over the past twenty years.
However, methods of elastic shape analysis are seldom utilized in practical applications
on real-world data, especially outside of the mathematical shape analysis community.
Our aim in this thesis is to explore some practical applications of elastic shape analysis.
To do this, we work with various types of shape data, the majority of which are based on
image datasets. As our focus is on two-dimensional curves, it is important to be able to
robustly extract contours from images, before we can apply elastic shape analysis tools.
In order to analyse the shapes in a dataset, we turn to methods of machine learning, to
investigate the applications of elastic shape analysis in classification.
In this thesis, we introduce an anthology of projects, in order to emphasise and under-
stand the potential of elastic shape analysis in practical applications. There are four main
projects in this thesis: (i) Classification of objects using outlines and the comparisons
between methods of elastic shape analysis, geometric morphometrics, and human experts,
with a focus on ancient Greek vases, (ii) Mussel species identification and a demonstra-
tion that shape may not be enough in some applications, (iii) A novel tool to monitor
the development of k Ì„ak Ì„ap Ì„o chicks, and (iv) Classifying individual kiwi based on acoustic
data from their calls.
By combining tools from computer vision and machine learning with methods of elastic
shape analysis, we introduce a practical framework for the application of elastic shape
analysis, through a data science lens
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