81 research outputs found
Curvilinear object segmentation in medical images based on ODoS filter and deep learning network
Automatic segmentation of curvilinear objects in medical images plays an
important role in the diagnosis and evaluation of human diseases, yet it is a
challenging uncertainty in the complex segmentation tasks due to different
issues such as various image appearances, low contrast between curvilinear
objects and their surrounding backgrounds, thin and uneven curvilinear
structures, and improper background illumination conditions. To overcome these
challenges, we present a unique curvilinear structure segmentation framework
based on an oriented derivative of stick (ODoS) filter and a deep learning
network for curvilinear object segmentation in medical images. Currently, a
large number of deep learning models emphasize developing deep architectures
and ignore capturing the structural features of curvilinear objects, which may
lead to unsatisfactory results. Consequently, a new approach that incorporates
an ODoS filter as part of a deep learning network is presented to improve the
spatial attention of curvilinear objects. Specifically, the input image is
transfered into four-channel image constructed by the ODoS filter. In which,
the original image is considered the principal part to describe various image
appearance and complex background illumination conditions, a multi-step
strategy is used to enhance the contrast between curvilinear objects and their
surrounding backgrounds, and a vector field is applied to discriminate thin and
uneven curvilinear structures. Subsequently, a deep learning framework is
employed to extract various structural features for curvilinear object
segmentation in medical images. The performance of the computational model is
validated in experiments conducted on the publicly available DRIVE, STARE and
CHASEDB1 datasets. The experimental results indicate that the presented model
yields surprising results compared with those of some state-of-the-art methods.Comment: 20 pages, 8 figure
Open-source virtual bronchoscopy for image guided navigation
This thesis describes the development of an open-source system for virtual bronchoscopy used in combination with electromagnetic instrument tracking. The end application is virtual navigation of the lung for biopsy of early stage cancer nodules. The open-source platform 3D Slicer was used for creating freely available algorithms for virtual bronchscopy. Firstly, the development of an open-source semi-automatic algorithm for prediction of solitary pulmonary nodule malignancy is presented. This approach may help the physician decide whether to proceed with biopsy of the nodule. The user-selected nodule is segmented in order to extract radiological characteristics (i.e., size, location, edge smoothness, calcification presence, cavity wall thickness) which are combined with patient information to calculate likelihood of malignancy. The overall accuracy of the algorithm is shown to be high compared to independent experts' assessment of malignancy. The algorithm is also compared with two different predictors, and our approach is shown to provide the best overall prediction accuracy. The development of an airway segmentation algorithm which extracts the airway tree from surrounding structures on chest Computed Tomography (CT) images is then described. This represents the first fundamental step toward the creation of a virtual bronchoscopy system. Clinical and ex-vivo images are used to evaluate performance of the algorithm. Different CT scan parameters are investigated and parameters for successful airway segmentation are optimized. Slice thickness is the most affecting parameter, while variation of reconstruction kernel and radiation dose is shown to be less critical. Airway segmentation is used to create a 3D rendered model of the airway tree for virtual navigation. Finally, the first open-source virtual bronchoscopy system was combined with electromagnetic tracking of the bronchoscope for the development of a GPS-like system for navigating within the lungs. Tools for pre-procedural planning and for helping with navigation are provided. Registration between the lungs of the patient and the virtually reconstructed airway tree is achieved using a landmark-based approach. In an attempt to reduce difficulties with registration errors, we also implemented a landmark-free registration method based on a balanced airway survey. In-vitro and in-vivo testing showed good accuracy for this registration approach. The centreline of the 3D airway model is extracted and used to compensate for possible registration errors. Tools are provided to select a target for biopsy on the patient CT image, and pathways from the trachea towards the selected targets are automatically created. The pathways guide the physician during navigation, while distance to target information is updated in real-time and presented to the user. During navigation, video from the bronchoscope is streamed and presented to the physician next to the 3D rendered image. The electromagnetic tracking is implemented with 5 DOF sensing that does not provide roll rotation information. An intensity-based image registration approach is implemented to rotate the virtual image according to the bronchoscope's rotations. The virtual bronchoscopy system is shown to be easy to use and accurate in replicating the clinical setting, as demonstrated in the pre-clinical environment of a breathing lung method. Animal studies were performed to evaluate the overall system performance
Quantitative lung CT analysis for the study and diagnosis of Chronic Obstructive Pulmonary Disease
The importance of medical imaging in the research of Chronic Obstructive Pulmonary Dis- ease (COPD) has risen over the last decades. COPD affects the pulmonary system through two competing mechanisms; emphysema and small airways disease. The relative contribu- tion of each component varies widely across patients whilst they can also evolve regionally in the lung. Patients can also be susceptible to exacerbations, which can dramatically ac- celerate lung function decline. Diagnosis of COPD is based on lung function tests, which measure airflow limitation. There is a growing consensus that this is inadequate in view of the complexities of COPD. Computed Tomography (CT) facilitates direct quantification of the pathological changes that lead to airflow limitation and can add to our understanding of the disease progression of COPD. There is a need to better capture lung pathophysiology whilst understanding regional aspects of disease progression. This has motivated the work presented in this thesis. Two novel methods are proposed to quantify the severity of COPD from CT by analysing the global distribution of features sampled locally in the lung. They can be exploited in the classification of lung CT images or to uncover potential trajectories of disease progression. A novel lobe segmentation algorithm is presented that is based on a probabilistic segmen- tation of the fissures whilst also constructing a groupwise fissure prior. In combination with the local sampling methods, a pipeline of analysis was developed that permits a re- gional analysis of lung disease. This was applied to study exacerbation susceptible COPD. Lastly, the applicability of performing disease progression modelling to study COPD has been shown. Two main subgroups of COPD were found, which are consistent with current clinical knowledge of COPD subtypes. This research may facilitate precise phenotypic characterisation of COPD from CT, which will increase our understanding of its natural history and associated heterogeneities. This will be instrumental in the precision medicine of COPD
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Knowledge graph applications in medical imaging analysis : a scoping review
There is an increasing trend to represent domain knowledge in structured graphs, which provide efficient knowledge representations for many downstream tasks. Knowledge graphs are widely used to model prior knowledge in the form of nodes and edges to represent semantically connected knowledge entities, which several works have adopted into different medical imaging applications. We systematically search over five databases to find relevant articles that apply knowledge graphs to medical imaging analysis. After screening, evaluating, and reviewing the selected articles, we performed a systematic analysis. We look at four applications in medical imaging analysis, including disease classification, disease localization and segmentation, report generation, and image retrieval. We also identify limitations of current work, such as the limited amount of available annotated data and weak generalizability to other tasks. We further identify the potential future directions according to the identified limitations, including employing semi-supervised frameworks to alleviate the need for annotated data and exploring task-agnostic models to provide better generalizability. We hope that our article will provide the readers with aggregated documentation of the state-of-the-art knowledge graph applications for medical imaging.Electrical and Computer Engineerin
Impurities Detection in Intensity Inhomogeneous Edible Bird’s Nest (EBN) Using a U-Net Deep Learning Model
As an important export, cleanliness control on edible bird’s nest (EBN) is paramount. Automatic impurities detection is in urgent need to replace manual practices. However, effective impurities detection algorithm is yet to be developed due to the unresolved inhomogeneous optical properties of EBN. The objective of this work is to develop a novel U-net based algorithm for accurate impurities detection. The algorithm leveraged the convolution mechanisms of U-net for precise and localized features extraction. Output probability tensors were then generated from the deconvolution layers for impurities detection and positioning. The U-net based algorithm outperformed previous image processing-based methods with a higher impurities detection rate of 96.69% and a lower misclassification rate of 10.08%. The applicability of the algorithm was further confirmed with a reasonably high dice coefficient of more than 0.8. In conclusion, the developed U-net based algorithm successfully mitigated intensity inhomogeneity in EBN and improved the impurities detection rate
Deep Learning with Limited Labels for Medical Imaging
Recent advancements in deep learning-based AI technologies provide an automatic tool to revolutionise medical image computing. Training a deep learning model requires a large amount of labelled data. Acquiring labels for medical images is extremely challenging due to the high cost in terms of both money and time, especially for the pixel-wise segmentation task of volumetric medical scans. However, obtaining unlabelled medical scans is relatively easier compared to acquiring labels for those images.
This work addresses the pervasive issue of limited labels in training deep learning models for medical imaging. It begins by exploring different strategies of entropy regularisation in the joint training of labelled and unlabelled data to reduce the time and cost associated with manual labelling for medical image segmentation. Of particular interest are consistency regularisation and pseudo labelling. Specifically, this work proposes a well-calibrated semi-supervised segmentation framework that utilises consistency regularisation on different morphological feature perturbations, representing a significant step towards safer AI in medical imaging. Furthermore, it reformulates pseudo labelling in semi-supervised learning as an Expectation-Maximisation framework. Building upon this new formulation, the work explains the empirical successes of pseudo labelling and introduces a generalisation of the technique, accompanied by variational inference to learn its true posterior distribution. The applications of pseudo labelling in segmentation tasks are also presented. Lastly, this work explores unsupervised deep learning for parameter estimation of diffusion MRI signals, employing a hierarchical variational clustering framework and representation learning
Hepatic Surgery
Longmire, called it a "hostile" organ because it welcomes malignant cells and sepsis so warmly, bleeds so copiously, and is often the ?rst organ to be injured in blunt abdominal trauma. To balance these negative factors, the liver has two great attributes: its ability to regenerate after massive loss of substance, and its ability, in many cases, to forgive insult. This book covers a wide spectrum of topics including, history of liver surgery, surgical anatomy of the liver, techniques of liver resection, benign and malignant liver tumors, portal hypertension, and liver trauma. Some important topics were covered in more than one chapter like liver trauma, portal hypertension and pediatric liver tumors
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