6,707 research outputs found
NiftyNet: a deep-learning platform for medical imaging
Medical image analysis and computer-assisted intervention problems are
increasingly being addressed with deep-learning-based solutions. Established
deep-learning platforms are flexible but do not provide specific functionality
for medical image analysis and adapting them for this application requires
substantial implementation effort. Thus, there has been substantial duplication
of effort and incompatible infrastructure developed across many research
groups. This work presents the open-source NiftyNet platform for deep learning
in medical imaging. The ambition of NiftyNet is to accelerate and simplify the
development of these solutions, and to provide a common mechanism for
disseminating research outputs for the community to use, adapt and build upon.
NiftyNet provides a modular deep-learning pipeline for a range of medical
imaging applications including segmentation, regression, image generation and
representation learning applications. Components of the NiftyNet pipeline
including data loading, data augmentation, network architectures, loss
functions and evaluation metrics are tailored to, and take advantage of, the
idiosyncracies of medical image analysis and computer-assisted intervention.
NiftyNet is built on TensorFlow and supports TensorBoard visualization of 2D
and 3D images and computational graphs by default.
We present 3 illustrative medical image analysis applications built using
NiftyNet: (1) segmentation of multiple abdominal organs from computed
tomography; (2) image regression to predict computed tomography attenuation
maps from brain magnetic resonance images; and (3) generation of simulated
ultrasound images for specified anatomical poses.
NiftyNet enables researchers to rapidly develop and distribute deep learning
solutions for segmentation, regression, image generation and representation
learning applications, or extend the platform to new applications.Comment: Wenqi Li and Eli Gibson contributed equally to this work. M. Jorge
Cardoso and Tom Vercauteren contributed equally to this work. 26 pages, 6
figures; Update includes additional applications, updated author list and
formatting for journal submissio
Feature Lines for Illustrating Medical Surface Models: Mathematical Background and Survey
This paper provides a tutorial and survey for a specific kind of illustrative
visualization technique: feature lines. We examine different feature line
methods. For this, we provide the differential geometry behind these concepts
and adapt this mathematical field to the discrete differential geometry. All
discrete differential geometry terms are explained for triangulated surface
meshes. These utilities serve as basis for the feature line methods. We provide
the reader with all knowledge to re-implement every feature line method.
Furthermore, we summarize the methods and suggest a guideline for which kind of
surface which feature line algorithm is best suited. Our work is motivated by,
but not restricted to, medical and biological surface models.Comment: 33 page
The Data Big Bang and the Expanding Digital Universe: High-Dimensional, Complex and Massive Data Sets in an Inflationary Epoch
Recent and forthcoming advances in instrumentation, and giant new surveys,
are creating astronomical data sets that are not amenable to the methods of
analysis familiar to astronomers. Traditional methods are often inadequate not
merely because of the size in bytes of the data sets, but also because of the
complexity of modern data sets. Mathematical limitations of familiar algorithms
and techniques in dealing with such data sets create a critical need for new
paradigms for the representation, analysis and scientific visualization (as
opposed to illustrative visualization) of heterogeneous, multiresolution data
across application domains. Some of the problems presented by the new data sets
have been addressed by other disciplines such as applied mathematics,
statistics and machine learning and have been utilized by other sciences such
as space-based geosciences. Unfortunately, valuable results pertaining to these
problems are mostly to be found only in publications outside of astronomy. Here
we offer brief overviews of a number of concepts, techniques and developments,
some "old" and some new. These are generally unknown to most of the
astronomical community, but are vital to the analysis and visualization of
complex datasets and images. In order for astronomers to take advantage of the
richness and complexity of the new era of data, and to be able to identify,
adopt, and apply new solutions, the astronomical community needs a certain
degree of awareness and understanding of the new concepts. One of the goals of
this paper is to help bridge the gap between applied mathematics, artificial
intelligence and computer science on the one side and astronomy on the other.Comment: 24 pages, 8 Figures, 1 Table. Accepted for publication: "Advances in
Astronomy, special issue "Robotic Astronomy
Model-Based Visualization for Intervention Planning
Computer support for intervention planning is often a two-stage process: In a first stage, the relevant segmentation target structures are identified and delineated. In a second stage, image analysis results are employed for the actual planning process. In the first stage, model-based segmentation techniques are often used to reduce the interaction effort and increase the reproducibility. There is a similar argument to employ model-based techniques for the visualization as well. With increasingly more visualization options, users have many parameters to adjust in order to generate expressive visualizations. Surface models may be smoothed with a variety of techniques and parameters. Surface visualization and illustrative rendering techniques are controlled by a large set of additional parameters. Although interactive 3d visualizations should be flexible and support individual planning tasks, appropriate selection of visualization techniques and presets for their parameters is needed. In this chapter, we discuss this kind of visualization support. We refer to model-based visualization to denote the selection and parameterization of visualization techniques based on \u27a priori knowledge concerning visual perception, shapes of anatomical objects and intervention planning tasks
Fuzzy Fibers: Uncertainty in dMRI Tractography
Fiber tracking based on diffusion weighted Magnetic Resonance Imaging (dMRI)
allows for noninvasive reconstruction of fiber bundles in the human brain. In
this chapter, we discuss sources of error and uncertainty in this technique,
and review strategies that afford a more reliable interpretation of the
results. This includes methods for computing and rendering probabilistic
tractograms, which estimate precision in the face of measurement noise and
artifacts. However, we also address aspects that have received less attention
so far, such as model selection, partial voluming, and the impact of
parameters, both in preprocessing and in fiber tracking itself. We conclude by
giving impulses for future research
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