438 research outputs found
2D View Aggregation for Lymph Node Detection Using a Shallow Hierarchy of Linear Classifiers
Enlarged lymph nodes (LNs) can provide important information for cancer
diagnosis, staging, and measuring treatment reactions, making automated
detection a highly sought goal. In this paper, we propose a new algorithm
representation of decomposing the LN detection problem into a set of 2D object
detection subtasks on sampled CT slices, largely alleviating the curse of
dimensionality issue. Our 2D detection can be effectively formulated as linear
classification on a single image feature type of Histogram of Oriented
Gradients (HOG), covering a moderate field-of-view of 45 by 45 voxels. We
exploit both simple pooling and sparse linear fusion schemes to aggregate these
2D detection scores for the final 3D LN detection. In this manner, detection is
more tractable and does not need to perform perfectly at instance level (as
weak hypotheses) since our aggregation process will robustly harness collective
information for LN detection. Two datasets (90 patients with 389 mediastinal
LNs and 86 patients with 595 abdominal LNs) are used for validation.
Cross-validation demonstrates 78.0% sensitivity at 6 false positives/volume
(FP/vol.) (86.1% at 10 FP/vol.) and 73.1% sensitivity at 6 FP/vol. (87.2% at 10
FP/vol.), for the mediastinal and abdominal datasets respectively. Our results
compare favorably to previous state-of-the-art methods.Comment: This article will be presented at MICCAI (Medical Image Computing and
Computer-Assisted Intervention) 201
Deep Domain Adaptation Learning Framework for Associating Image Features to Tumour Gene Profile
While medical imaging and general pathology are routine in cancer diagnosis, genetic sequencing is not always assessable due to the strong phenotypic and genetic heterogeneity of human cancers. Image-genomics integrates medical imaging and genetics to provide a complementary approach to optimise cancer diagnosis by associating tumour imaging traits with clinical data and has demonstrated its potential in identifying imaging surrogates for tumour biomarkers. However, existing image-genomics research has focused on quantifying tumour visual traits according to human understanding, which may not be optimal across different cancer types. The challenge hence lies in the extraction of optimised imaging representations in an objective data-driven manner. Such an approach requires large volumes of annotated image data that are difficult to acquire. We propose a deep domain adaptation learning framework for associating image features to tumour genetic information, exploiting the ability of domain adaptation technique to learn relevant image features from close knowledge domains. Our proposed framework leverages the current state-of-the-art in image object recognition to provide image features to encode subtle variations of tumour phenotypic characteristics with domain adaptation techniques. The proposed framework was evaluated with current state-of-the-art in: (i) tumour histopathology image classification and; (ii) image-genomics associations. The proposed framework demonstrated improved accuracy of tumour classification, as well as providing additional data-derived representations of tumour phenotypic characteristics that exhibit strong image-genomics association. This thesis advances and indicates the potential of image-genomics research to reveal additional imaging surrogates to genetic biomarkers, which has the potential to facilitate cancer diagnosis
Machine Learning/Deep Learning in Medical Image Processing
Many recent studies on medical image processing have involved the use of machine learning (ML) and deep learning (DL). This special issue, “Machine Learning/Deep Learning in Medical Image Processing”, has been launched to provide an opportunity for researchers in the area of medical image processing to highlight recent developments made in their fields with ML/DL. Seven excellent papers that cover a wide variety of medical/clinical aspects are selected in this special issue
Digital image processing for prognostic and diagnostic clinical pathology
When digital imaging and image processing methods are applied to clinical diagnostic
and prognostic needs, the methods can be seen to increase human understanding and
provide objective measurements. Most current clinical applications are limited to
providing subjective information to healthcare professionals rather than providing
objective measures. This Thesis provides detail of methods and systems that have been
developed both for objective and subjective microscopy applications. A system
framework is presented that provides a base for the development of microscopy imaging
systems. This practical framework is based on currently available hardware and
developed with standard software development tools. Image processing methods are
applied to counter optical limitations of the bright field microscope, automating the
system and allowing for unsupervised image capture and analysis.
Current literature provides evidence that 3D visualisation has provided increased
insight and application in many clinical areas. There have been recent advancements in
the use of 3D visualisation for the study of soft tissue structures, but its clinical
application within histology remains limited. Methods and applications have been
researched and further developed which allow for the 3D reconstruction and
visualisation of soft tissue structures using microtomed serial histological sections
specimens. A system has been developed suitable for this need is presented giving
considerations to image capture, data registration and 3D visualisation, requirements.
The developed system has been used to explore and increase 3D insight on clinical
samples.
The area of automated objective image quantification of microscope slides
presents the allure of providing objective methods replacing existing objective and
subjective methods, increasing accuracy and rsducinq manual burden. One such
existing objective test is DNA Image Ploidy which seeks to characterise cancer by the
measurement of DNA content within individual cell nuclei, an accepted but manually
burdensome method. The main novelty of the work completed lies in the development of
an automated system for DNA Image Ploidy measurement, combining methods for
automatic specimen focus, segmentation, parametric extraction and the implementation
of an automated cell type classification system.
A consideration for any clinical image processing system is the correct sampling
of the tissue under study. VVhile the image capture requirements for both objective
systems and subjective systems are similar there is also an important link between the
3D structures of the tissue. 3D understanding can aid in decisions regarding the
sampling criteria of objective tests for as although many tests are completed in the 2D
realm the clinical samples are 3D objects. Cancers such as Prostate and Breast cancer
are known to be multi-focal, with areas of seeming physically, independent areas of
disease within a single site. It is not possible to understand the true 3D nature of the
samples using 2D micro-tomed sections in isolation from each other. The 3D systems
described in this report provide a platform of the exploration of the true multi focal nature
of disease soft tissue structures allowing for the sampling criteria of objective tests such
as DNA Image Ploidy to be correctly set.
For the Automated DNA Image Ploidy and the 3D reconstruction and
visualisation systems, clinical review has been completed to test the increased insights
provided. Datasets which have been reconstructed from microtomed serial sections and
visualised with the developed 3D system area presented. For the automated DNA Image
Ploidy system, the developed system is compared with the existing manual method to
qualify the quality of data capture, operational speed and correctness of nuclei
classification.
Conclusions are presented for the work that has been completed and discussion
given as to future areas of research that could be undertaken, extending the areas of
study, increasing both clinical insight and practical application
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