Automatic Pancreas Segmentation and 3D Reconstruction for Morphological Feature Extraction in Medical Image Analysis

The development of highly accurate, quantitative automatic medical image segmentation techniques, in comparison to manual techniques, remains a constant challenge for medical image analysis. In particular, segmenting the pancreas from an abdominal scan presents additional difficulties: this particular organ has very high anatomical variability, and a full inspection is problematic due to the location of the pancreas behind the stomach. Therefore, accurate, automatic pancreas segmentation can consequently yield quantitative morphological measures such as volume and curvature, supporting biomedical research to establish the severity and progression of a condition, such as type 2 diabetes mellitus. Furthermore, it can also guide subject stratification after diagnosis or before clinical trials, and help shed additional light on detecting early signs of pancreatic cancer. This PhD thesis delivers a novel approach for automatic, accurate quantitative pancreas segmentation in mostly but not exclusively Magnetic Resonance Imaging (MRI), by harnessing the advantages of machine learning and classical image processing in computer vision. The proposed approach is evaluated on two MRI datasets containing 216 and 132 image volumes, achieving a mean Dice similarity coefficient (DSC) of 84:1 4:6% and 85:7 2:3% respectively. In order to demonstrate the universality of the approach, a dataset containing 82 Computer Tomography (CT) image volumes is also evaluated and achieves mean DSC of 83:1 5:3%. The proposed approach delivers a contribution to computer science (computer vision) in medical image analysis, reporting better quantitative pancreas segmentation results in comparison to other state-of-the-art techniques, and also captures detailed pancreas boundaries as verified by two independent experts in radiology and radiography. The contributions’ impact can support the usage of computational methods in biomedical research with a clinical translation; for example, the pancreas volume provides a prognostic biomarker about the severity of type 2 diabetes mellitus. Furthermore, a generalisation of the proposed segmentation approach successfully extends to other anatomical structures, including the kidneys, liver and iliopsoas muscles using different MRI sequences. Thus, the proposed approach can incorporate into the development of a computational tool to support radiological interpretations of MRI scans obtained using different sequences by providing a “second opinion”, help reduce possible misdiagnosis, and consequently, provide enhanced guidance towards targeted treatment planning

Semi-inclusive charged-pion electroproduction off protons and deuterons: Cross sections, ratios, and access to the quark-parton model at low energies

A large set of cross sections for semi-inclusive electroproduction of charged pions (π^±) from both proton and deuteron targets was measured. The data are in the deep-inelastic scattering region with invariant mass squared W^2>4 GeV^2 (up to ≈7 GeV^2) and range in four-momentum transfer squared 2<Q^2<4 (GeV/c)^2, and cover a range in the Bjorken scaling variable 0.2<x<0.6. The fractional energy of the pions spans a range 0.3<z<1, with small transverse momenta with respect to the virtual-photon direction, Pt^(2)_(t)<0.2 (GeV/c)2. The invariant mass that goes undetected, M_x or W′, is in the nucleon resonance region, W′<2 GeV. The new data conclusively show the onset of quark-hadron duality in this process, and the relation of this phenomenon to the high-energy factorization ansatz of electron-quark scattering and subsequent quark→pion production mechanisms. The x, z, and Pt^(2)_(t) dependences of several ratios (the ratios of favored-unfavored fragmentation functions, charged pion ratios, deuteron-hydrogen and aluminum-deuteron ratios for π^+ and π^−) have been studied. The ratios are found to be in good agreement with expectations based upon a high-energy quark-parton model description. We find the azimuthal dependences to be small, as compared to exclusive pion electroproduction, and consistent with theoretical expectations based on tree-level factorization in terms of transverse-momentum-dependent parton distribution and fragmentation functions. In the context of a simple model, the initial transverse momenta of d quarks are found to be slightly smaller than for u quarks, while the transverse momentum width of the favored fragmentation function is about the same as for the unfavored one, and both fragmentation widths are larger than the quark widths

Hierarchical Framework for Automatic Pancreas Segmentation in MRI Using Continuous Max-flow and Min-Cuts Approach

Accurate, automatic and robust segmentation of the pancreas in medical image scans remains a challenging but important prerequisite for computer-aided diagnosis (CADx). This paper presents a tool for automatic pancreas segmentation in magnetic resonance imaging (MRI) scans. Proposed is a framework that employs a hierarchical pooling of information as follows: identify major pancreas region and apply contrast enhancement to differentiate between pancreatic and surrounding tissue; perform 3D segmentation by employing continuous max-flow and min-cuts approach, structured forest edge detection, and a training dataset of annotated pancreata; eliminate non-pancreatic contours from resultant segmentation via morphological operations on area, curvature and position between distinct contours. The proposed method is evaluated on a dataset of 20 MRI volumes, achieving a mean Dice Similarity coefficient of 75.5 ± 7.0% and a mean Jaccard Index coefficient of 61.2 ± 9.2%

AI Driven IoT Web-Based Application for Automatic Segmentation and Reconstruction of Abdominal Organs from Medical Images

Medical imaging technology has rapidly advanced in the last few decades, providing detailed images of the human body. The accurate analysis of these images and the segmentation of anatomical structures can produce significant morphological information, provide additional guidance toward subject stratification after diagnosis or before a clinical trial, and help predict a medical condition. Usually, medical scans are manually segmented by expert operators, such as radiologists and radiographers, which is complex, time-consuming and prone to inter-observer variability. A system that generates automatic, accurate quantitative organ segmentation on a large scale could deliver a clinical impact, supporting current investigations in subjects with medical conditions and aiding early diagnosis and treatment planning. This paper proposes a web-based application that automatically segments multiple abdominal organs and muscle, produces respective 3D reconstructions and extracts valuable biomarkers using a deep learning backend engine. Furthermore, it is possible to upload image data and access the medical image segmentation tool without installation using any device connected to the Internet. The final aim is to deliver a web- based image-processing service that clinical experts, researchers and users can seamlessly access through IoT devices without requiring knowledge of the underpinning technology

Morphological and multi-level geometrical descriptor analysis in CT and MRI volumes for automatic pancreas segmentation

Automatic pancreas segmentation in 3D radiological scans is a critical, yet challenging task. As a prerequisite for computer-aided diagnosis (CADx) systems, accurate pancreas segmentation could generate both quantitative and qualitative information towards establishing the severity of a condition, and thus provide additional guidance for therapy planning. Since the pancreas is an organ of high inter-patient anatomical variability, previous segmentation approaches report lower quantitative accuracy scores in comparison to abdominal organs such as the liver or kidneys. This paper presents a novel approach for automatic pancreas segmentation in magnetic resonance imaging (MRI) and computer tomography (CT) scans. This method exploits 3D segmentation that, when coupled with geometrical and morphological characteristics of abdominal tissue, classifies distinct contours in tight pixel-range proximity as “pancreas” or “non-pancreas”. There are three main stages to this approach: (1) identify a major pancreas region and apply contrast enhancement to differentiate between pancreatic and surrounding tissue; (2) perform 3D segmentation via continuous max-flow and min-cuts approach, structured forest edge detection, and a training dataset of annotated pancreata; (3) eliminate non-pancreatic contours from resultant segmentation via morphological operations on area, structure and connectivity between distinct contours. The proposed method is evaluated on a dataset containing 82 CT image volumes, achieving mean Dice Similarity coefficient (DSC) of 79.3 ± 4.4%. Two MRI datasets containing 216 and 132 image volumes are evaluated, achieving mean DSC 79.6 ± 5.7% and 81.6 ± 5.1% respectively. This approach is statistically stable, reflected by lower metrics in standard deviation in comparison to state-of-the-art approaches

A Framework for Automatic Morphological Feature Extraction and Analysis of Abdominal Organs in MRI Volumes

The accurate 3D reconstruction of organs from radiological scans is an essential tool in computer-aided diagnosis (CADx) and plays a critical role in clinical, biomedical and forensic science research. The structure and shape of the organ, combined with morphological measurements such as volume and curvature, can provide significant guidance towards establishing progression or severity of a condition, and thus support improved diagnosis and therapy planning. Furthermore, the classification and stratification of organ abnormalities aim to explore and investigate organ deformations following injury, trauma and illness. This paper presents a framework for automatic morphological feature extraction in computer-aided 3D organ reconstructions following organ segmentation in 3D radiological scans. Two different magnetic resonance imaging (MRI) datasets are evaluated. Using the MRI scans of 85 adult volunteers, the overall mean volume for the pancreas organ is 69.30 ± 32.50cm3, and the 3D global curvature is (35.23 ± 6.83) × 10−3. Another experiment evaluates the MRI scans of 30 volunteers, and achieves mean liver volume of 1547.48 ± 204.19cm3 and 3D global curvature (19.87 ± 3.62) × 10− 3. Both experiments highlight a negative correlation between 3D curvature and volume with a statistical difference (p < 0.0001). Such a tool can support the investigation into organ related conditions such as obesity, type 2 diabetes mellitus and liver disease

A Framework for Morphological Feature Extraction of Organs from MR Images for Detection and Classification of Abnormalities

In clinical practice, a misdiagnosis can lead to incorrect or delayed treatment, and in some cases, no treatment at all; consequently, the condition of a patient may worsen to varying degrees, in some cases proving fatal. The accurate 3D reconstruction of organs, which is a pioneering tool of medical image computing (MIC) technology, plays a key role in computer aided diagnosis (CADx), thereby enabling medical professionals to perform enhanced analysis on a region of interest. From here, the shape and structure of the organ coupled with measurements of its volume and curvature can provide significant guidance towards establishing the severity of a disorder or abnormality, consequently supporting improved diagnosis and treatment planning. Moreover, the classification and stratification of organ abnormalities is widely utilised within biomedical, forensic and MIC research for exploring and investigating organ deformations following injury, illness or trauma. This paper presents a tool that calculates, classifies and analyses pancreatic volume and curvature following their 3D reconstruction. Magnetic resonance imaging (MRI) volumes of 115 adult patients are evaluated in order to examine a correlation between these two variables. Such a tool can be utilised in the scope of much greater research and investigation. It can also be incorporated into the development of effective medical image analysis software application in the stratification of subjects and targeting of therapies

Improving the accuracy of fatty liver index to reflect liver fat content with predictive regression modelling

The fatty liver index (FLI) is frequently used as a non-invasive clinical marker for research, prognostic and diagnostic purposes. It is also used to stratify individuals with hepatic steatosis such as non-alcoholic fatty liver disease (NAFLD), and to detect the presence of type 2 diabetes or cardiovascular disease. The FLI is calculated using a combination of anthropometric and blood biochemical variables; however, it reportedly excludes 8.5-16.7% of individuals with NAFLD. Moreover, the FLI cannot quantitatively predict liver fat, which might otherwise render an improved diagnosis and assessment of fatty liver, particularly in longitudinal studies. We propose FLI+ using predictive regression modelling, an improved index reflecting liver fat content that integrates 12 routinely-measured variables, including the original FLI. Methods and findings: We evaluated FLI+ on a dataset from the UK Biobank containing 28,796 individual estimates of proton density fat fraction derived from magnetic resonance imaging across normal to severe levels and interpolated to align with the original FLI range. The results obtained for FLI+ outperform the original FLI by delivering a lower mean absolute error by approximately 47%, a lower standard deviation by approximately 20%, and an increased adjusted R2 statistic by approximately 49%, reflecting a more accurate representation of liver fat content. Conclusions: Our proposed model predicting FLI+ has the potential to improve diagnosis and provide a more accurate stratification than FLI between absent, mild, moderate and severe levels of hepatic steatosis

3D Deep Learning for Anatomical Structure Segmentation in Multiple Imaging Modalities

Accurate, automated quantitative segmentation of anatomical structures in radiological scans, such as Magnetic Resonance Imaging (MRI) and Computer Tomography (CT), can produce significant biomarkers and can be integrated into computer-aided diagnosis (CADx) systems to support the in- terpretation of medical images from multi-protocol scanners. However, there are serious challenges towards developing robust automated segmentation techniques, including high variations in anatomical structure and size, varying image spatial resolutions resulting from different scanner protocols, and the presence of blurring artefacts. This paper presents a novel computing ap- proach for automated organ and muscle segmentation in medical images from multiple modalities by harnessing the advantages of deep learning techniques in a two-part process. (1) a 3D encoder-decoder, Rb-UNet, builds a localisation model and a 3D Tiramisu network generates a boundary-preserving segmentation model for each target structure; (2) the fully trained Rb-UNet predicts a 3D bounding box encapsulating the target structure of interest, after which the fully trained Tiramisu model performs segmentation to reveal organ or muscle boundaries for every protrusion and indentation. The proposed approach is evaluated on six different datasets, including MRI, Dynamic Contrast Enhanced (DCE) MRI and CT scans targeting the pancreas, liver, kidneys and iliopsoas muscles. We achieve quantitative measures of mean Dice similarity coefficient (DSC) that surpasses or are comparable with the state-of-the-art and demonstrate statistical stability. A qualitative evaluation performed by two independent experts in radiology and radiography verified the preservation of detailed organ and muscle boundaries

Advancing Pancreas Segmentation in Multi-protocol MRI Volumes using Hausdorff-Sine Loss Function

Computing pancreatic morphology in 3D radiological scans could provide significant insight about a medical condition. However, segmenting the pancreas in magnetic resonance imaging (MRI) remains challenging due to high inter-patient variability. Also, the resolution and speed of MRI scanning present artefacts that blur the pancreas bound- aries between overlapping anatomical structures. This paper proposes a dual-stage automatic segmentation method: 1) a deep neural network is trained to address the problem of vague organ boundaries in high class-imbalanced data. This network integrates a novel loss function to rigorously optimise boundary delineation using the modified Hausdorff metric and a sinusoidal component; 2) Given a test MRI volume, the output of the trained network predicts a sequence of targeted 2D pan- creas classes that are reconstructed as a volumetric binary mask. An energy-minimisation approach fuses a learned digital contrast model to suppress the intensities of non-pancreas classes, which, combined with the binary volume performs a refined segmentation in 3D while reveal- ing dense boundary detail. Experiments are performed on two diverse MRI datasets containing 180 and 120 scans, in which the proposed ap- proach achieves a mean Dice score of 84.1 ± 4.6% and 85.7 ± 2.3%, respectively. This approach is statistically stable and outperforms state- of-the-art methods on MRI