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Segmentation and density estimation in femur
Horáček, Jan ; Maršálek, Lukáš (advisor)
Title: Segmentation and Density Estimation in Femur Author: Jan Horáček Department: Department of Software and Computer Science Education Supervisor: Mgr. Lukáš Maršálek Supervisor's e-mail address: lukas.marsalek@mff.cuni.cz Abstract: There are two basic ways of surgical treatment of femoral neck frac- ture - total endoprosthesis or a special metal screw in the bone. In case of a dense enough bone the screws are preferred. But for a too sparse bone, the screw may cut through the femoral head, which results in further surgical operations. We present a novel method for femoral head density measurement, which serves as another hint for the doctor's decision, whether to apply a screw or total endo- prosthesis. Our approach is based on semi-automatical femoral head segmenta- tion from CT dataset based on finding optimal path through polar coordinates on axial slices. The cost function is based on a combination of corticallis proper- ties, mostly the directional behavior of 3D gradients and their size in 2D slices, where they form typical "channels". The final volume is computed using filling and morphological algorithms and its properties are further measured. The final implementation was experimentally validated on RTG clinic of Bulovka hospital and allows radiologists to intuitively and accurately estimate...
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Interactive 3D CT Data Segmentation Based on Deep Learning
Trávníčková, Kateřina ; Hradiš, Michal (referee) ; Kodym, Oldřich (advisor)
This thesis deals with CT data segmentation using convolutional neural nets and describes the problem of training with limited training sets. User interaction is suggested as means of improving segmentation quality for the models trained on small training sets and the possibility of using transfer learning is also considered. All of the chosen methods help improve the segmentation quality in comparison with the baseline method, which is the use of automatic data specific segmentation model. The segmentation has improved by tens of percents in Dice score when trained with very small datasets. These methods can be used, for example, to simplify the creation of a new segmentation dataset.
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Displaying 3D Graphics in Web Browser
Sychra, Tomáš ; Pečiva, Jan (referee) ; Španěl, Michal (advisor)
This thesis discusses possibilities of accelerated 3D scene displaying in a Web browser. In more detail, it deals with WebGL standard and its use in real applications. An application for visualization of volumetric medical data based on JavaScript, WebGL and Three.js library was designed and implemented. Image data are loaded from Google Drive cloud storage. An important part of the application is 3D visualization of the volumetric data based on volume rendering technique called Ray-casting.
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Hybrid renderer
Goliaš, Matúš ; Pelikán, Josef (advisor) ; Horáček, Jan (referee)
Title: Hybrid renderer Author: Matúš Goliaš Department: Department of Software and Computer Science Education Supervisor: RNDr. Josef Pelikán, KSVI Abstract: In medical applications, there are often used both volume data and objects defined by their surface. However, rendering these two types of data together is rather dif- ficult. This thesis provides the description of ray marching algorithm for volume rendering. We base the algorithm on the emission-absorption model of light trans- fer through a gaseous material. Moreover, we discuss the problems of adding meshes to the volume with respect to the algorithm. Next, we propose an ex- tension of ray marching which takes all meshes into account and renders them with the volume correctly. In addition, we compare the individual approaches for solving steps of the algorithm. Finally, we implement our solution in an ap- plication for volume viewing. We develop this renderer using OpenGL and we discuss our options of implementation. Furthermore, we extend our application by allowing the camera inside the volume, clipping the scene and interactive edit- ing of transfer functions which define the colour representation of volume data. Subsequently, we describe every feature and discuss its possible implementations. Keywords: volume data, ray marching, translucent...
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Correspondence Problem in Geometrics Morphometric Tasks
Krajíček, Václav ; Pelikán, Josef (advisor) ; Kosinka, Jiří (referee) ; Sochor, Jiří (referee)
Title: Correspondence Problem in Geometric Morphometrics Tasks Author: Václav Krajíček Department / Institute: Department of Software and Computer Science Education Supervisor of the doctoral thesis: RNDr. Josef Pelikán Supervisor's e-mail address: pepca@cgg.mff.cuni.cz Abstract: Shape analysis in physical anthropology, biomedicine, and related disci- plines is mostly done using landmarks or by measuring distances. New techno- logical advancements allow the digitization of object's appearance in the form of triangular meshes or volume images. These digital images are especially beneficial in the cases when landmarks cannot be used to effectively describe the shape. In order to statistically analyze shape in a sample of observations, which are represented by these modalities, correspondence has to be found. Registration is a crucial tool in mapping the shape representations into a common space where correspondence is found by nearest neighbor principle in the case of triangular meshes or by overlaps in the case of volume images. B- spline based non-rigid registration is chosen because of its versatility, relative speed and ability to handle both meshes and volume images. Experiments were also performed with other alternatives - Thin-plate splines and Coherent point drift. The algorithm was modified to handle...
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Multidimensional transfer functions for scalar volumetric data visualization
Mach, Pavel ; Kolomazník, Jan (advisor) ; Dupej, Ján (referee)
Direct volume rendering is an algorithm used for displaying three-dimensional scalar data, like image from Computed Tomography. This algorithm makes use of a concept of Transfer functions for assigning optical properties to the data values. We studied two dimensional transfer functions, that besides primary values have additional dataset as an input. In particular, we studied computation of this secondary dataset with respect to the primary image function shape. This was done by analysing eigenvalues of the Hessian matrix in each image point. We proposed one formula and implemented several others for computing the probability that image point belongs to the blood vessel. Powered by TCPDF (www.tcpdf.org)
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Segmentation and density estimation in femur
Horáček, Jan ; Maršálek, Lukáš (advisor)
Title: Segmentation and Density Estimation in Femur Author: Jan Horáček Department: Department of Software and Computer Science Education Supervisor: Mgr. Lukáš Maršálek Supervisor's e-mail address: lukas.marsalek@mff.cuni.cz Abstract: There are two basic ways of surgical treatment of femoral neck frac- ture - total endoprosthesis or a special metal screw in the bone. In case of a dense enough bone the screws are preferred. But for a too sparse bone, the screw may cut through the femoral head, which results in further surgical operations. We present a novel method for femoral head density measurement, which serves as another hint for the doctor's decision, whether to apply a screw or total endo- prosthesis. Our approach is based on semi-automatical femoral head segmenta- tion from CT dataset based on finding optimal path through polar coordinates on axial slices. The cost function is based on a combination of corticallis proper- ties, mostly the directional behavior of 3D gradients and their size in 2D slices, where they form typical "channels". The final volume is computed using filling and morphological algorithms and its properties are further measured. The final implementation was experimentally validated on RTG clinic of Bulovka hospital and allows radiologists to intuitively and accurately estimate...
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Volume data editor
Kavalík, Jiří ; Kolomazník, Jan (referee) ; Krajíček, Václav (advisor)
In the present work we want to design and implement simple tool for basic editing of volume data like resizing, rotating, tresholding retouching, which could be extended as needed. Currently, there are tools for volume data visualisation and simple editors for modding computer games with voxel-based graphics. There is not an editor with basic set of tools for editing volumes in resolution of medical scanners available to common user. The designed and implemented editor can run on common hardware and oth ers set of simple brushes and filters to the user and means to implement diferent tools as plugins for C# programmer.
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