399 research outputs found
A Survey on Deep Learning in Medical Image Analysis
Deep learning algorithms, in particular convolutional networks, have rapidly
become a methodology of choice for analyzing medical images. This paper reviews
the major deep learning concepts pertinent to medical image analysis and
summarizes over 300 contributions to the field, most of which appeared in the
last year. We survey the use of deep learning for image classification, object
detection, segmentation, registration, and other tasks and provide concise
overviews of studies per application area. Open challenges and directions for
future research are discussed.Comment: Revised survey includes expanded discussion section and reworked
introductory section on common deep architectures. Added missed papers from
before Feb 1st 201
Optic nerve head segmentation
Reliable and efficient optic disk localization and segmentation are important tasks in automated retinal screening. General-purpose edge detection algorithms often fail to segment the optic disk due to fuzzy boundaries, inconsistent image contrast or missing edge features. This paper presents an algorithm for the localization and segmentation of the optic nerve head boundary in low-resolution images (about 20 /spl mu//pixel). Optic disk localization is achieved using specialized template matching, and segmentation by a deformable contour model. The latter uses a global elliptical model and a local deformable model with variable edge-strength dependent stiffness. The algorithm is evaluated against a randomly selected database of 100 images from a diabetic screening programme. Ten images were classified as unusable; the others were of variable quality. The localization algorithm succeeded on all bar one usable image; the contour estimation algorithm was qualitatively assessed by an ophthalmologist as having Excellent-Fair performance in 83% of cases, and performs well even on blurred image
Medical image registration using unsupervised deep neural network: A scoping literature review
In medicine, image registration is vital in image-guided interventions and
other clinical applications. However, it is a difficult subject to be addressed
which by the advent of machine learning, there have been considerable progress
in algorithmic performance has recently been achieved for medical image
registration in this area. The implementation of deep neural networks provides
an opportunity for some medical applications such as conducting image
registration in less time with high accuracy, playing a key role in countering
tumors during the operation. The current study presents a comprehensive scoping
review on the state-of-the-art literature of medical image registration studies
based on unsupervised deep neural networks is conducted, encompassing all the
related studies published in this field to this date. Here, we have tried to
summarize the latest developments and applications of unsupervised deep
learning-based registration methods in the medical field. Fundamental and main
concepts, techniques, statistical analysis from different viewpoints,
novelties, and future directions are elaborately discussed and conveyed in the
current comprehensive scoping review. Besides, this review hopes to help those
active readers, who are riveted by this field, achieve deep insight into this
exciting field
Modeling Brain Circuitry over a Wide Range of Scales
If we are ever to unravel the mysteries of brain function at its most
fundamental level, we will need a precise understanding of how its component
neurons connect to each other. Electron Microscopes (EM) can now provide the
nanometer resolution that is needed to image synapses, and therefore
connections, while Light Microscopes (LM) see at the micrometer resolution
required to model the 3D structure of the dendritic network. Since both the
topology and the connection strength are integral parts of the brain's wiring
diagram, being able to combine these two modalities is critically important.
In fact, these microscopes now routinely produce high-resolution imagery in
such large quantities that the bottleneck becomes automated processing and
interpretation, which is needed for such data to be exploited to its full
potential. In this paper, we briefly review the Computer Vision techniques we
have developed at EPFL to address this need. They include delineating dendritic
arbors from LM imagery, segmenting organelles from EM, and combining the two
into a consistent representation
Deep convolutional neural networks for segmenting 3D in vivo multiphoton images of vasculature in Alzheimer disease mouse models
The health and function of tissue rely on its vasculature network to provide
reliable blood perfusion. Volumetric imaging approaches, such as multiphoton
microscopy, are able to generate detailed 3D images of blood vessels that could
contribute to our understanding of the role of vascular structure in normal
physiology and in disease mechanisms. The segmentation of vessels, a core image
analysis problem, is a bottleneck that has prevented the systematic comparison
of 3D vascular architecture across experimental populations. We explored the
use of convolutional neural networks to segment 3D vessels within volumetric in
vivo images acquired by multiphoton microscopy. We evaluated different network
architectures and machine learning techniques in the context of this
segmentation problem. We show that our optimized convolutional neural network
architecture, which we call DeepVess, yielded a segmentation accuracy that was
better than both the current state-of-the-art and a trained human annotator,
while also being orders of magnitude faster. To explore the effects of aging
and Alzheimer's disease on capillaries, we applied DeepVess to 3D images of
cortical blood vessels in young and old mouse models of Alzheimer's disease and
wild type littermates. We found little difference in the distribution of
capillary diameter or tortuosity between these groups, but did note a decrease
in the number of longer capillary segments () in aged animals as
compared to young, in both wild type and Alzheimer's disease mouse models.Comment: 34 pages, 9 figure
Intersubject Regularity in the Intrinsic Shape of Human V1
Previous studies have reported considerable intersubject variability in the three-dimensional geometry of the human primary visual cortex (V1). Here we demonstrate that much of this variability is due to extrinsic geometric features of the cortical folds, and that the intrinsic shape of V1 is similar across individuals. V1 was imaged in ten ex vivo human hemispheres using high-resolution (200 μm) structural magnetic resonance imaging at high field strength (7 T). Manual tracings of the stria of Gennari were used to construct a surface representation, which was computationally flattened into the plane with minimal metric distortion. The instrinsic shape of V1 was determined from the boundary of the planar representation of the stria. An ellipse provided a simple parametric shape model that was a good approximation to the boundary of flattened V1. The aspect ration of the best-fitting ellipse was found to be consistent across subject, with a mean of 1.85 and standard deviation of 0.12. Optimal rigid alignment of size-normalized V1 produced greater overlap than that achieved by previous studies using different registration methods. A shape analysis of published macaque data indicated that the intrinsic shape of macaque V1 is also stereotyped, and similar to the human V1 shape. Previoud measurements of the functional boundary of V1 in human and macaque are in close agreement with these results
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