4189
2013
eng
reportzib
0
2013-07-30
2013-07-30
--
Fast Generation of Virtual X-ray Images from Deformable Tetrahedral Meshes
We propose a novel GPU-based approach to render virtual X-ray projections of deformable tetrahedral meshes. These meshes represent the shape and the internal density distribution of a particular anatomical structure and are derived from statistical shape and intensity models (SSIMs). We apply our method to improve the geometric reconstruction of 3D anatomy (e.g.\ pelvic bone) from 2D X-ray images. For that purpose, shape and density of a tetrahedral mesh are varied and virtual X-ray projections are generated within an optimization process until the similarity between the computed virtual X-ray and the respective anatomy depicted in a given clinical X-ray is maximized. The OpenGL implementation presented in this work deforms and projects tetrahedral meshes of high resolution (200.000+ tetrahedra) at interactive rates. It generates virtual X-rays that accurately depict the density distribution of an anatomy of interest. Compared to existing methods that accumulate X-ray attenuation in deformable meshes, our novel approach significantly boosts the deformation/projection performance. The proposed projection algorithm scales better with respect to mesh resolution and complexity of the density distribution, and the combined deformation and projection on the GPU scales better with respect to the number of deformation parameters. The gain in performance allows for a larger number of cycles in the optimization process. Consequently, it reduces the risk of being stuck in a local optimum. We believe that our approach contributes in orthopedic surgery, where 3D anatomy information needs to be extracted from 2D X-rays to support surgeons in better planning joint replacements.
1438-0064
urn:nbn:de:0297-zib-41896
no
appeared in IEEE Transactions on Visualization and Computer Graphics
Moritz Ehlke
Moritz Ehlke
Heiko Ramm
Hans Lamecker
Hans-Christian Hege
Stefan Zachow
ZIB-Report
13-38
eng
uncontrolled
digitally reconstructed radiographs
eng
uncontrolled
volume rendering
eng
uncontrolled
mesh deformation
eng
uncontrolled
statistical shape and intensity models
eng
uncontrolled
image registration
eng
uncontrolled
GPU acceleration
Computing Methodologies
COMPUTER SCIENCE (For papers involving machine computations and programs in a specific mathematical area, see Section -04 in that area)
Visual Data Analysis
Visual Data Analysis in Science and Engineering
Therapy Planning
Ehlke, Moritz
Hege, Hans-Christian
Lamecker, Hans
Zachow, Stefan
BSRT-3DFromXray
Visual and Data-centric Computing
https://opus4.kobv.de/opus4-zib/files/4189/Report-13-38.pdf
1434
2011
eng
reportzib
0
2011-12-19
2011-12-19
--
Perception-Oriented Picking of Structures in Direct Volumetric Renderings
Radiologists from all application areas are trained to read slice-based visualizations of 3D medical image data. Despite the numerous
examples of sophisticated three-dimensional renderings, especially all variants of direct volume rendering, such methods are
often considered not very useful by radiologists who prefer slice-based visualization. Just recently there have been attempts to bridge this
gap between 2D and 3D renderings. These attempts include specialized techniques for volume picking that result in repositioning slices.
In this paper, we present a new volume picking technique that, in contrast to previous work, does not require pre-segmented data or metadata. The positions picked by our method are solely based on the data itself, the transfer function and,
most importantly, on the way the volumetric rendering is perceived by viewers. To demonstrate the usefulness of the proposed method
we apply it for automatically
repositioning slices in an abdominal MRI
scan, a data set from a flow simulation and a number of other volumetric scalar fields. Furthermore we discuss how the method can be implemented in combination with various different volumetric rendering techniques.
1438-0064
11-45
urn:nbn:de:0297-zib-14343
no
Alexander Wiebel
Alexander Wiebel
Frans M. Vos
Hans-Christian Hege
ZIB-Report
11-45
eng
uncontrolled
DVR
eng
uncontrolled
picking
eng
uncontrolled
pointing
eng
uncontrolled
direct volume rendering
PHYSICAL SCIENCES AND ENGINEERING
LIFE AND MEDICAL SCIENCES
COMPUTER SCIENCE (For papers involving machine computations and programs in a specific mathematical area, see Section -04 in that area)
Visual Data Analysis
Hege, Hans-Christian
VIGOR++
Visual and Data-centric Computing
https://opus4.kobv.de/opus4-zib/files/1434/result.pdf
6182
eng
reportzib
0
--
2017-01-25
--
Revealing hidden text in rolled and folded papyri
Ancient Egyptian papyri are often folded, rolled up or kept as small packages, sometimes even sealed. Physically unrolling or unfolding these packages might severely damage them. We demonstrate a way to get access to the hidden script without physical unfolding by employing computed tomography and mathematical algorithms for virtual unrolling and unfolding. Our algorithmic approaches are combined with manual interaction. This provides the necessary flexibility to enable the unfolding of even complicated and partly damaged papyrus packages. In addition, it allows us to cope with challenges posed by the structure of ancient papyrus, which is rather irregular, compared to other writing substrates like metallic foils or parchment. Unfolding of packages is done in two stages. In the first stage, we virtually invert the physical folding process step by step until the partially unfolded package is topologically equivalent to a scroll or a papyrus sheet folded only along one fold line. To minimize distortions at this stage, we apply the method of moving least squares. In the second stage, the papyrus is simply flattened, which requires the definition of a medial surface. We have applied our software framework to several papyri. In this work, we present the results of applying our approaches to mockup papyri that were either rolled or folded along perpendicular fold lines. In the case of the folded papyrus, our approach represents the first attempt to address the unfolding of such complicated folds.
1438-0064
urn:nbn:de:0297-zib-61826
10.1007/s00339-017-0808-6
Appeared in: Applied Physics A 123 (2017) pp. 171
Daniel Baum
Daniel Baum
Norbert Lindow
Hans-Christian Hege
Verena Lepper
Tzulia Siopi
Frank Kutz
Kristin Mahlow
Heinz-Eberhard Mahnke
ZIB-Report
17-02
eng
uncontrolled
unfolding, papyri, computed tomography
Computer Applications
INTERDISCIPLINARY PHYSICS AND RELATED AREAS OF SCIENCE AND TECHNOLOGY
COMPUTER SCIENCE (For papers involving machine computations and programs in a specific mathematical area, see Section -04 in that area)
Visual Data Analysis
Baum, Daniel
Hege, Hans-Christian
Lindow, Norbert
no-project
Visual and Data-centric Computing
https://opus4.kobv.de/opus4-zib/files/6182/ZR-17-02.pdf
4315
2013
2013
eng
reportzib
0
2013-11-29
--
--
The Filament Editor: An Interactive Software Environment for Visualization, Proof-Editing and Analysis of 3D Neuron Morphology
Neuroanatomical analysis, such as classification of cell types, depends on reliable reconstruction of large numbers of complete 3D dendrite and axon morphologies. At present, the majority of neuron reconstructions are obtained from preparations in a single tissue slice in vitro, thus suffering from cut off dendrites and, more dramatically, cut off axons. In general, axons can innervate volumes of several cubic millimeters and may reach path lengths of tens of centimeters. Thus, their complete reconstruction requires in vivo labeling, histological sectioning and imaging of large fields of view. Unfortunately, anisotropic background conditions across such large tissue volumes, as well as faintly labeled thin neurites, result in incomplete or erroneous automated tracings and even lead experts to make annotation errors during manual reconstructions. Consequently, tracing reliability renders the major bottleneck for reconstructing complete 3D neuron morphologies. Here, we present a novel set of tools, integrated into a software environment named ‘Filament Editor’, for creating reliable neuron tracings from sparsely labeled in vivo datasets. The Filament Editor allows for simultaneous visualization of complex neuronal tracings and image data in a 3D viewer, proof-editing of neuronal tracings, alignment and interconnection across sections, and morphometric analysis in relation to 3D anatomical reference structures. We illustrate the functionality of the Filament Editor on the example of in vivo labeled axons and demonstrate that for the exemplary dataset the final tracing results after proof-editing are independent of the expertise of the human operator.
1438-0064
urn:nbn:de:0297-zib-43157
10.1007/s12021-013-9213-2
Neuroinformatics 12(2), pp 325-339, 2014
no
Vincent J. Dercksen
Vincent J. Dercksen
Hans-Christian Hege
Marcel Oberlaender
ZIB-Report
13-75
Software
COMPUTER SCIENCE (For papers involving machine computations and programs in a specific mathematical area, see Section -04 in that area)
Visual Data Analysis
Visual Data Analysis in Science and Engineering
Hege, Hans-Christian
Neuro
Visual and Data-centric Computing
https://opus4.kobv.de/opus4-zib/files/4315/ZR-13-75.pdf