32,314 research outputs found
Computerized Analysis of Magnetic Resonance Images to Study Cerebral Anatomy in Developing Neonates
The study of cerebral anatomy in developing neonates is of great importance for
the understanding of brain development during the early period of life. This
dissertation therefore focuses on three challenges in the modelling of cerebral
anatomy in neonates during brain development. The methods that have been
developed all use Magnetic Resonance Images (MRI) as source data.
To facilitate study of vascular development in the neonatal period, a set of image
analysis algorithms are developed to automatically extract and model cerebral
vessel trees. The whole process consists of cerebral vessel tracking from
automatically placed seed points, vessel tree generation, and vasculature
registration and matching. These algorithms have been tested on clinical Time-of-
Flight (TOF) MR angiographic datasets.
To facilitate study of the neonatal cortex a complete cerebral cortex segmentation
and reconstruction pipeline has been developed. Segmentation of the neonatal
cortex is not effectively done by existing algorithms designed for the adult brain
because the contrast between grey and white matter is reversed. This causes pixels
containing tissue mixtures to be incorrectly labelled by conventional methods. The
neonatal cortical segmentation method that has been developed is based on a novel
expectation-maximization (EM) method with explicit correction for mislabelled
partial volume voxels. Based on the resulting cortical segmentation, an implicit
surface evolution technique is adopted for the reconstruction of the cortex in
neonates. The performance of the method is investigated by performing a detailed
landmark study.
To facilitate study of cortical development, a cortical surface registration algorithm
for aligning the cortical surface is developed. The method first inflates extracted
cortical surfaces and then performs a non-rigid surface registration using free-form
deformations (FFDs) to remove residual alignment. Validation experiments using
data labelled by an expert observer demonstrate that the method can capture local
changes and follow the growth of specific sulcus
On Using Physical Analogies for Feature and Shape Extraction in Computer Vision
There is a rich literature of approaches to image feature extraction in computer vision. Many sophisticated approaches exist for low- and high-level feature extraction but can be complex to implement with parameter choice guided by experimentation, but impeded by speed of computation. We have developed new ways to extract features based on notional use of physical paradigms, with parameterisation that is more familiar to a scientifically-trained user, aiming to make best use of computational resource. We describe how analogies based on gravitational force can be used for low-level analysis, whilst analogies of water flow and heat can be deployed to achieve high-level smooth shape detection. These new approaches to arbitrary shape extraction are compared with standard state-of-art approaches by curve evolution. There is no comparator operator to our use of gravitational force. We also aim to show that the implementation is consistent with the original motivations for these techniques and so contend that the exploration of physical paradigms offers a promising new avenue for new approaches to feature extraction in computer vision
A graph theoretic approach to scene matching
The ability to match two scenes is a fundamental requirement in a variety of computer vision tasks. A graph theoretic approach to inexact scene matching is presented which is useful in dealing with problems due to imperfect image segmentation. A scene is described by a set of graphs, with nodes representing objects and arcs representing relationships between objects. Each node has a set of values representing the relations between pairs of objects, such as angle, adjacency, or distance. With this method of scene representation, the task in scene matching is to match two sets of graphs. Because of segmentation errors, variations in camera angle, illumination, and other conditions, an exact match between the sets of observed and stored graphs is usually not possible. In the developed approach, the problem is represented as an association graph, in which each node represents a possible mapping of an observed region to a stored object, and each arc represents the compatibility of two mappings. Nodes and arcs have weights indicating the merit or a region-object mapping and the degree of compatibility between two mappings. A match between the two graphs corresponds to a clique, or fully connected subgraph, in the association graph. The task is to find the clique that represents the best match. Fuzzy relaxation is used to update the node weights using the contextual information contained in the arcs and neighboring nodes. This simplifies the evaluation of cliques. A method of handling oversegmentation and undersegmentation problems is also presented. The approach is tested with a set of realistic images which exhibit many types of sementation errors
Deep Interactive Region Segmentation and Captioning
With recent innovations in dense image captioning, it is now possible to
describe every object of the scene with a caption while objects are determined
by bounding boxes. However, interpretation of such an output is not trivial due
to the existence of many overlapping bounding boxes. Furthermore, in current
captioning frameworks, the user is not able to involve personal preferences to
exclude out of interest areas. In this paper, we propose a novel hybrid deep
learning architecture for interactive region segmentation and captioning where
the user is able to specify an arbitrary region of the image that should be
processed. To this end, a dedicated Fully Convolutional Network (FCN) named
Lyncean FCN (LFCN) is trained using our special training data to isolate the
User Intention Region (UIR) as the output of an efficient segmentation. In
parallel, a dense image captioning model is utilized to provide a wide variety
of captions for that region. Then, the UIR will be explained with the caption
of the best match bounding box. To the best of our knowledge, this is the first
work that provides such a comprehensive output. Our experiments show the
superiority of the proposed approach over state-of-the-art interactive
segmentation methods on several well-known datasets. In addition, replacement
of the bounding boxes with the result of the interactive segmentation leads to
a better understanding of the dense image captioning output as well as accuracy
enhancement for the object detection in terms of Intersection over Union (IoU).Comment: 17, pages, 9 figure
Cell Segmentation and Tracking using CNN-Based Distance Predictions and a Graph-Based Matching Strategy
The accurate segmentation and tracking of cells in microscopy image sequences
is an important task in biomedical research, e.g., for studying the development
of tissues, organs or entire organisms. However, the segmentation of touching
cells in images with a low signal-to-noise-ratio is still a challenging
problem. In this paper, we present a method for the segmentation of touching
cells in microscopy images. By using a novel representation of cell borders,
inspired by distance maps, our method is capable to utilize not only touching
cells but also close cells in the training process. Furthermore, this
representation is notably robust to annotation errors and shows promising
results for the segmentation of microscopy images containing in the training
data underrepresented or not included cell types. For the prediction of the
proposed neighbor distances, an adapted U-Net convolutional neural network
(CNN) with two decoder paths is used. In addition, we adapt a graph-based cell
tracking algorithm to evaluate our proposed method on the task of cell
tracking. The adapted tracking algorithm includes a movement estimation in the
cost function to re-link tracks with missing segmentation masks over a short
sequence of frames. Our combined tracking by detection method has proven its
potential in the IEEE ISBI 2020 Cell Tracking Challenge
(http://celltrackingchallenge.net/) where we achieved as team KIT-Sch-GE
multiple top three rankings including two top performances using a single
segmentation model for the diverse data sets.Comment: 25 pages, 14 figures, methods of the team KIT-Sch-GE for the IEEE
ISBI 2020 Cell Tracking Challeng
- …