52,018 research outputs found
Numerical simulation of the stress-strain state of the dental system
We present mathematical models, computational algorithms and software, which
can be used for prediction of results of prosthetic treatment. More interest
issue is biomechanics of the periodontal complex because any prosthesis is
accompanied by a risk of overloading the supporting elements. Such risk can be
avoided by the proper load distribution and prediction of stresses that occur
during the use of dentures. We developed the mathematical model of the
periodontal complex and its software implementation. This model is based on
linear elasticity theory and allows to calculate the stress and strain fields
in periodontal ligament and jawbone. The input parameters for the developed
model can be divided into two groups. The first group of parameters describes
the mechanical properties of periodontal ligament, teeth and jawbone (for
example, elasticity of periodontal ligament etc.). The second group
characterized the geometric properties of objects: the size of the teeth, their
spatial coordinates, the size of periodontal ligament etc. The mechanical
properties are the same for almost all, but the input of geometrical data is
complicated because of their individual characteristics. In this connection, we
develop algorithms and software for processing of images obtained by computed
tomography (CT) scanner and for constructing individual digital model of the
tooth-periodontal ligament-jawbone system of the patient. Integration of models
and algorithms described allows to carry out biomechanical analysis on
three-dimensional digital model and to select prosthesis design.Comment: 19 pages, 9 figure
Scale Stain: Multi-Resolution Feature Enhancement in Pathology Visualization
Digital whole-slide images of pathological tissue samples have recently
become feasible for use within routine diagnostic practice. These gigapixel
sized images enable pathologists to perform reviews using computer workstations
instead of microscopes. Existing workstations visualize scanned images by
providing a zoomable image space that reproduces the capabilities of the
microscope. This paper presents a novel visualization approach that enables
filtering of the scale-space according to color preference. The visualization
method reveals diagnostically important patterns that are otherwise not
visible. The paper demonstrates how this approach has been implemented into a
fully functional prototype that lets the user navigate the visualization
parameter space in real time. The prototype was evaluated for two common
clinical tasks with eight pathologists in a within-subjects study. The data
reveal that task efficiency increased by 15% using the prototype, with
maintained accuracy. By analyzing behavioral strategies, it was possible to
conclude that efficiency gain was caused by a reduction of the panning needed
to perform systematic search of the images. The prototype system was well
received by the pathologists who did not detect any risks that would hinder use
in clinical routine
Software for full-color 3D reconstruction of the biological tissues internal structure
A software for processing sets of full-color images of biological tissue
histological sections is developed. We used histological sections obtained by
the method of high-precision layer-by-layer grinding of frozen biological
tissues. The software allows restoring the image of the tissue for an arbitrary
cross-section of the tissue sample. Thus, our method is designed to create a
full-color 3D reconstruction of the biological tissue structure. The resolution
of 3D reconstruction is determined by the quality of the initial histological
sections. The newly developed technology available to us provides a resolution
of up to 5 - 10 {\mu}m in three dimensions.Comment: 11 pages, 8 figure
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
Computational medical imaging for total knee arthroplasty using visualitzation toolkit
This project is presented as a Master Thesis in the field of Civil Engineering, Biomedical specialization. As the
project of an Erasmus exchange student, this thesis has been under supervision both the Universite Livre de
Bruxelles and the Universitat Politecnica de Catalunya. The purpose of this thesis to put in practice all the
knowledges acquired during this Master in Industrial Engineering in UPC and to be a support for medical staff
in total knee arthoplasty procedures.
Prof. Emmanuel Thienpont has been working for years as orthopaedic surgeon at the Hospital Sant Luc,
Brussels. His years of work and research have been mainly focused on Total Knee Arthroplasty or TKA. During
one of the most important steps of this procedure, the orthopaedic surgeon has to cut the head of the femur
following two perpendicular cutting planes. Nevertheless, the orientation of these planes are directly dependant
of the femur constitution.
This Master Thesis has been conceived in order to offer the surgeon a tool to determine the proper direction
planes in a previous step before the surgical procedure. This project pretends to give the surgeon an openfree
computational platform to access to patient geometrical and physiological information before involving the
subject in any invasive procedure
MITK-ModelFit: A generic open-source framework for model fits and their exploration in medical imaging -- design, implementation and application on the example of DCE-MRI
Many medical imaging techniques utilize fitting approaches for quantitative
parameter estimation and analysis. Common examples are pharmacokinetic modeling
in DCE MRI/CT, ADC calculations and IVIM modeling in diffusion-weighted MRI and
Z-spectra analysis in chemical exchange saturation transfer MRI. Most available
software tools are limited to a special purpose and do not allow for own
developments and extensions. Furthermore, they are mostly designed as
stand-alone solutions using external frameworks and thus cannot be easily
incorporated natively in the analysis workflow. We present a framework for
medical image fitting tasks that is included in MITK, following a rigorous
open-source, well-integrated and operating system independent policy. Software
engineering-wise, the local models, the fitting infrastructure and the results
representation are abstracted and thus can be easily adapted to any model
fitting task on image data, independent of image modality or model. Several
ready-to-use libraries for model fitting and use-cases, including fit
evaluation and visualization, were implemented. Their embedding into MITK
allows for easy data loading, pre- and post-processing and thus a natural
inclusion of model fitting into an overarching workflow. As an example, we
present a comprehensive set of plug-ins for the analysis of DCE MRI data, which
we validated on existing and novel digital phantoms, yielding competitive
deviations between fit and ground truth. Providing a very flexible environment,
our software mainly addresses developers of medical imaging software that
includes model fitting algorithms and tools. Additionally, the framework is of
high interest to users in the domain of perfusion MRI, as it offers
feature-rich, freely available, validated tools to perform pharmacokinetic
analysis on DCE MRI data, with both interactive and automatized batch
processing workflows.Comment: 31 pages, 11 figures URL: http://mitk.org/wiki/MITK-ModelFi
Volumetric visualization of 3D data
In recent years, there has been a rapid growth in the ability to obtain detailed data on large complex structures in three dimensions. This development occurred first in the medical field, with CAT (computer aided tomography) scans and now magnetic resonance imaging, and in seismological exploration. With the advances in supercomputing and computational fluid dynamics, and in experimental techniques in fluid dynamics, there is now the ability to produce similar large data fields representing 3D structures and phenomena in these disciplines. These developments have produced a situation in which currently there is access to data which is too complex to be understood using the tools available for data reduction and presentation. Researchers in these areas are becoming limited by their ability to visualize and comprehend the 3D systems they are measuring and simulating
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