VCBM 14: Eurographics Workshop on Visual Computing for Biology and Medicine

Permanent URI for this collection

https://diglib7.eg.org/handle/10.2312/7762
Vienna, Austria, September 4 – 5, 2014

BibTeX (VCBM 14: Eurographics Workshop on Visual Computing for Biology and Medicine)
@inproceedings{
10.2312:vcbm.20141179,
http::/hdl.handle.net/10.2312/vcbm.20141179.001-009,

booktitle = {
Eurographics Workshop on Visual Computing for Biology and Medicine},

editor = {
Ivan Viola and Katja Buehler and Timo Ropinski
},
title = {{
Robust Cardiac Function Assessment in 4D PC-MRI Data}},

author = {
Köhler, Benjamin
 and 
Preim, Uta
 and 
Gutberlet, Matthias
 and 
Fischbach, Katharina
 and 
Preim, Bernhard
},
year = {
2014},

publisher = {
The Eurographics Association},


ISSN = {2070-5778},
ISBN = {978-3-905674-62-0},

DOI = {
10.2312/vcbm.20141179}
http://hdl.handle.net/10.2312/vcbm.20141179.001-009}

}
@inproceedings{
10.2312:vcbm.20141178,
http::/hdl.handle.net/10.2312/vcbm.20141178.011-020,

booktitle = {
Eurographics Workshop on Visual Computing for Biology and Medicine},

editor = {
Ivan Viola and Katja Buehler and Timo Ropinski
},
title = {{
The iCoCooN: Integration of Cobweb Charts with Parallel Coordinates for Visual Analysis of DCE-MRI Modeling Variations}},

author = {
Raidou, Renata G.
 and 
Breeuwer, Marcel
 and 
Vilanova, Anna
 and 
Heide, U. A. van der
 and 
Houdt, P. J. van
},
year = {
2014},

publisher = {
The Eurographics Association},


ISSN = {2070-5778},
ISBN = {978-3-905674-62-0},

DOI = {
10.2312/vcbm.20141178}
http://hdl.handle.net/10.2312/vcbm.20141178.011-020}

}
@inproceedings{
10.2312:vcbm.20141180,
http::/hdl.handle.net/10.2312/vcbm.20141180.021-030,

booktitle = {
Eurographics Workshop on Visual Computing for Biology and Medicine},

editor = {
Ivan Viola and Katja Buehler and Timo Ropinski
},
title = {{
A Survey on Visualizing Magnetic Resonance Spectroscopy Data}},

author = {
Nunes, Miguel
 and 
Laruelo, Andrea
 and 
Ken, SoleaKhena
 and 
Laprie, Anne
 and 
Bühler, Katja
},
year = {
2014},

publisher = {
The Eurographics Association},


ISSN = {2070-5778},
ISBN = {978-3-905674-62-0},

DOI = {
10.2312/vcbm.20141180}
http://hdl.handle.net/10.2312/vcbm.20141180.021-030}

}
@inproceedings{
10.2312:vcbm.20141181,
http::/hdl.handle.net/10.2312/vcbm.20141181.031-039,

booktitle = {
Eurographics Workshop on Visual Computing for Biology and Medicine},

editor = {
Ivan Viola and Katja Buehler and Timo Ropinski
},
title = {{
Extracting and Visualizing Uncertainties in Segmentations from 3D Medical Data}},

author = {
Faltin, Peter
 and 
Chaisaowong, Kraisorn
 and 
Kraus, Thomas
 and 
Merhof, Dorit
},
year = {
2014},

publisher = {
The Eurographics Association},


ISSN = {2070-5778},
ISBN = {978-3-905674-62-0},

DOI = {
10.2312/vcbm.20141181}
http://hdl.handle.net/10.2312/vcbm.20141181.031-039}

}
@inproceedings{
10.2312:vcbm.20141182,
http::/hdl.handle.net/10.2312/vcbm.20141182.041-050,

booktitle = {
Eurographics Workshop on Visual Computing for Biology and Medicine},

editor = {
Ivan Viola and Katja Buehler and Timo Ropinski
},
title = {{
Uncertainty-aware Ensemble of Classifiers for Segmenting Brain MRI Data}},

author = {
Al-Taie, Ahmed
 and 
Hahn, Horst K.
 and 
Linsen, Lars
},
year = {
2014},

publisher = {
The Eurographics Association},


ISSN = {2070-5778},
ISBN = {978-3-905674-62-0},

DOI = {
10.2312/vcbm.20141182}
http://hdl.handle.net/10.2312/vcbm.20141182.041-050}

}
@inproceedings{
10.2312:vcbm.20141183,
http::/hdl.handle.net/10.2312/vcbm.20141183.051-058,

booktitle = {
Eurographics Workshop on Visual Computing for Biology and Medicine},

editor = {
Ivan Viola and Katja Buehler and Timo Ropinski
},
title = {{
Inlier Detection in Thermal Sensitive Images}},

author = {
Zadicario, Eyal
 and 
Carmi, N.
 and 
Ju, Tao
 and 
Cohen-Or, Daniel
},
year = {
2014},

publisher = {
The Eurographics Association},


ISSN = {2070-5778},
ISBN = {978-3-905674-62-0},

DOI = {
10.2312/vcbm.20141183}
http://hdl.handle.net/10.2312/vcbm.20141183.051-058}

}
@inproceedings{
10.2312:vcbm.20141184,
http::/hdl.handle.net/10.2312/vcbm.20141184.059-068,

booktitle = {
Eurographics Workshop on Visual Computing for Biology and Medicine},

editor = {
Ivan Viola and Katja Buehler and Timo Ropinski
},
title = {{
Real-Time Dense Nucleus Selection from Confocal Data}},

author = {
Wan, Yong
 and 
Otsuna, Hideo
 and 
Kwan, K. M.
 and 
Hansen, Charles
},
year = {
2014},

publisher = {
The Eurographics Association},


ISSN = {2070-5778},
ISBN = {978-3-905674-62-0},

DOI = {
10.2312/vcbm.20141184}
http://hdl.handle.net/10.2312/vcbm.20141184.059-068}

}
@inproceedings{
10.2312:vcbm.20141185,
http::/hdl.handle.net/10.2312/vcbm.20141185.069-078,

booktitle = {
Eurographics Workshop on Visual Computing for Biology and Medicine},

editor = {
Ivan Viola and Katja Buehler and Timo Ropinski
},
title = {{
Imaging the Vascular Network of the Human Spleen from Immunostained Serial Sections}},

author = {
Ulrich, Christine
 and 
Lobachev, Oleg
 and 
Steiniger, Birte
 and 
Guthe, Michael
},
year = {
2014},

publisher = {
The Eurographics Association},


ISSN = {2070-5778},
ISBN = {978-3-905674-62-0},

DOI = {
10.2312/vcbm.20141185}
http://hdl.handle.net/10.2312/vcbm.20141185.069-078}

}
@inproceedings{
10.2312:vcbm.20141186,
http::/hdl.handle.net/10.2312/vcbm.20141186.079-088,

booktitle = {
Eurographics Workshop on Visual Computing for Biology and Medicine},

editor = {
Ivan Viola and Katja Buehler and Timo Ropinski
},
title = {{
Interactive Labeling of Toponome Data}},

author = {
Oeltze-Jafra, Steffen
 and 
Pieper, Franz
 and 
Hillert, Reyk
 and 
Preim, Bernhard
 and 
Schubert, Walter
},
year = {
2014},

publisher = {
The Eurographics Association},


ISSN = {2070-5778},
ISBN = {978-3-905674-62-0},

DOI = {
10.2312/vcbm.20141186}
http://hdl.handle.net/10.2312/vcbm.20141186.079-088}

}
@inproceedings{
10.2312:vcbm.20141187,
http::/hdl.handle.net/10.2312/vcbm.20141187.089-096,

booktitle = {
Eurographics Workshop on Visual Computing for Biology and Medicine},

editor = {
Ivan Viola and Katja Buehler and Timo Ropinski
},
title = {{
Membrane Mapping: Combining Mesoscopic and Molecular Cell Visualization}},

author = {
Waltemate, Thomas
 and 
Sommer, Björn
 and 
Botsch, Mario
},
year = {
2014},

publisher = {
The Eurographics Association},


ISSN = {2070-5778},
ISBN = {978-3-905674-62-0},

DOI = {
10.2312/vcbm.20141187}
http://hdl.handle.net/10.2312/vcbm.20141187.089-096}

}
@inproceedings{
10.2312:vcbm.20141188,
http::/hdl.handle.net/10.2312/vcbm.20141188.097-106,

booktitle = {
Eurographics Workshop on Visual Computing for Biology and Medicine},

editor = {
Ivan Viola and Katja Buehler and Timo Ropinski
},
title = {{
Visualizing Movements of Protein Tunnels in Molecular Dynamics Simulations}},

author = {
Kozlíková, Barbora
 and 
Jurcík, Adam
 and 
By ka, Jan
 and 
Strnad, Ondrej
 and 
Sochor, Jirí
},
year = {
2014},

publisher = {
The Eurographics Association},


ISSN = {2070-5778},
ISBN = {978-3-905674-62-0},

DOI = {
10.2312/vcbm.20141188}
http://hdl.handle.net/10.2312/vcbm.20141188.097-106}

}
@inproceedings{
10.2312:vcbm.20141189,
http::/hdl.handle.net/10.2312/vcbm.20141189.107-116,

booktitle = {
Eurographics Workshop on Visual Computing for Biology and Medicine},

editor = {
Ivan Viola and Katja Buehler and Timo Ropinski
},
title = {{
Visual and Quantitative Analysis of Higher Order Arborization Overlaps for Neural Circuit Research}},

author = {
Swoboda, Nicolas
 and 
Moosburner, Judith
 and 
Bruckner, Stefan
 and 
Yu, Jai Y.
 and 
Dickson, Barry J.
 and 
Bühler, Katja
},
year = {
2014},

publisher = {
The Eurographics Association},


ISSN = {2070-5778},
ISBN = {978-3-905674-62-0},

DOI = {
10.2312/vcbm.20141189}
http://hdl.handle.net/10.2312/vcbm.20141189.107-116}

}
@inproceedings{
10.2312:vcbm.20141197,
http::/hdl.handle.net/10.2312/vcbm.20141197.117-126,

booktitle = {
Eurographics Workshop on Visual Computing for Biology and Medicine},

editor = {
Ivan Viola and Katja Buehler and Timo Ropinski
},
title = {{
Evaluation of Transfer Function Methods in Direct Volume Rendering of the Blood Vessel Lumen}},

author = {
Läthén, Gunnar
 and 
Lindholm, Stefan
 and 
Lenz, Reiner
 and 
Borga, Magnus
},
year = {
2014},

publisher = {
The Eurographics Association},


ISSN = {2070-5778},
ISBN = {978-3-905674-62-0},

DOI = {
10.2312/vcbm.20141197}
http://hdl.handle.net/10.2312/vcbm.20141197.117-126}

}
@inproceedings{
10.2312:vcbm.20141198,
http::/hdl.handle.net/10.2312/vcbm.20141198.127-136,

booktitle = {
Eurographics Workshop on Visual Computing for Biology and Medicine},

editor = {
Ivan Viola and Katja Buehler and Timo Ropinski
},
title = {{
Visibility-Driven Processing of Streaming Volume Data}},

author = {
Solteszova, Veronika
 and 
Birkeland, Asmund
 and 
Viola, Ivan
 and 
Bruckner, Stefan
},
year = {
2014},

publisher = {
The Eurographics Association},


ISSN = {2070-5778},
ISBN = {978-3-905674-62-0},

DOI = {
10.2312/vcbm.20141198}
http://hdl.handle.net/10.2312/vcbm.20141198.127-136}

}
@inproceedings{
10.2312:vcbm.20141199,
http::/hdl.handle.net/10.2312/vcbm.20141199.137-143,

booktitle = {
Eurographics Workshop on Visual Computing for Biology and Medicine},

editor = {
Ivan Viola and Katja Buehler and Timo Ropinski
},
title = {{
Towards Clinical Deployment of Automated Anatomical Regions-Of-Interest}},

author = {
Lindholm, Stefan
 and 
Forsberg, Daniel
 and 
Ynnerman, Anders
 and 
Knutsson, Hans
 and 
Andersson, Mats
 and 
Lundström, Claes
},
year = {
2014},

publisher = {
The Eurographics Association},


ISSN = {2070-5778},
ISBN = {978-3-905674-62-0},

DOI = {
10.2312/vcbm.20141199}
http://hdl.handle.net/10.2312/vcbm.20141199.137-143}

}
@inproceedings{
10.2312:vcbm.20141194,
http::/hdl.handle.net/10.2312/vcbm.20141194.155-162,

booktitle = {
Eurographics Workshop on Visual Computing for Biology and Medicine},

editor = {
Ivan Viola and Katja Buehler and Timo Ropinski
},
title = {{
Personalized X-ray Reconstruction of the Proximal Femur via a New Control Point-based 2D-3D Registration and Residual Complexity Minimization}},

author = {
Yu, Weimin
 and 
Zheng, Guoyan
},
year = {
2014},

publisher = {
The Eurographics Association},


ISSN = {2070-5778},
ISBN = {978-3-905674-62-0},

DOI = {
10.2312/vcbm.20141194}
http://hdl.handle.net/10.2312/vcbm.20141194.155-162}

}
@inproceedings{
10.2312:vcbm.20141193,
http::/hdl.handle.net/10.2312/vcbm.20141193.145-153,

booktitle = {
Eurographics Workshop on Visual Computing for Biology and Medicine},

editor = {
Ivan Viola and Katja Buehler and Timo Ropinski
},
title = {{
RegistrationShop: An Interactive 3D Medical Volume Registration System}},

author = {
Smit, Noeska N.
 and 
Haneveld, Berend Klein
 and 
Staring, Marius
 and 
Eisemann, Elmar
 and 
Botha, Charl P.
 and 
Vilanova, Anna
},
year = {
2014},

publisher = {
The Eurographics Association},


ISSN = {2070-5778},
ISBN = {978-3-905674-62-0},

DOI = {
10.2312/vcbm.20141193}
http://hdl.handle.net/10.2312/vcbm.20141193.145-153}

}
@inproceedings{
10.2312:vcbm.20141195,
http::/hdl.handle.net/10.2312/vcbm.20141195.163-172,

booktitle = {
Eurographics Workshop on Visual Computing for Biology and Medicine},

editor = {
Ivan Viola and Katja Buehler and Timo Ropinski
},
title = {{
Misalignment Correction in Open Cone-Beam CT}},

author = {
Wieckowski, Adam
 and 
Stopp, Fabian
 and 
Käseberg, Marc
 and 
Keeve, Erwin
},
year = {
2014},

publisher = {
The Eurographics Association},


ISSN = {2070-5778},
ISBN = {978-3-905674-62-0},

DOI = {
10.2312/vcbm.20141195}
http://hdl.handle.net/10.2312/vcbm.20141195.163-172}

}
@inproceedings{
10.2312:vcbm.20141196,
http::/hdl.handle.net/10.2312/vcbm.20141196.173-180,

booktitle = {
Eurographics Workshop on Visual Computing for Biology and Medicine},

editor = {
Ivan Viola and Katja Buehler and Timo Ropinski
},
title = {{
Deriving Anatomical Context from 4D Ultrasound}},

author = {
Müller, Markus
 and 
Helljesen, Linn E. S.
 and 
Prevost, Raphael
 and 
Viola, Ivan
 and 
Nylund, Kim
 and 
Gilja, Odd Helge
 and 
Navab, Nassir
 and 
Wein, Wolfgang
},
year = {
2014},

publisher = {
The Eurographics Association},


ISSN = {2070-5778},
ISBN = {978-3-905674-62-0},

DOI = {
10.2312/vcbm.20141196}
http://hdl.handle.net/10.2312/vcbm.20141196.173-180}

}
@inproceedings{
10.2312:vcbm.20141190,
http::/hdl.handle.net/10.2312/vcbm.20141190.181-190,

booktitle = {
Eurographics Workshop on Visual Computing for Biology and Medicine},

editor = {
Ivan Viola and Katja Buehler and Timo Ropinski
},
title = {{
A Comparative User Study of a 2D and an Autostereoscopic 3D Display for a Tympanoplastic Surgery}},

author = {
Baer, Alexandra
 and 
Huebler, Antje
 and 
Saalfeld, Patrick
 and 
Cunningham, Douglas
 and 
Preim, Bernhard
},
year = {
2014},

publisher = {
The Eurographics Association},


ISSN = {2070-5778},
ISBN = {978-3-905674-62-0},

DOI = {
10.2312/vcbm.20141190}
http://hdl.handle.net/10.2312/vcbm.20141190.181-190}

}
@inproceedings{
10.2312:vcbm.20141192,
http::/hdl.handle.net/10.2312/vcbm.20141192.199-208,

booktitle = {
Eurographics Workshop on Visual Computing for Biology and Medicine},

editor = {
Ivan Viola and Katja Buehler and Timo Ropinski
},
title = {{
Survey of Labeling Techniques in Medical Visualizations}},

author = {
Oeltze-Jafra, Steffen
 and 
Preim, Bernhard
},
year = {
2014},

publisher = {
The Eurographics Association},


ISSN = {2070-5778},
ISBN = {978-3-905674-62-0},

DOI = {
10.2312/vcbm.20141192}
http://hdl.handle.net/10.2312/vcbm.20141192.199-208}

}
@inproceedings{
10.2312:vcbm.20141191,
http::/hdl.handle.net/10.2312/vcbm.20141191.191-198,

booktitle = {
Eurographics Workshop on Visual Computing for Biology and Medicine},

editor = {
Ivan Viola and Katja Buehler and Timo Ropinski
},
title = {{
Interactive Visualization of Muscle Activity During Limb Movements: Towards Enhanced Anatomy Learning}},

author = {
Bauer, Armelle
 and 
Paclet, Florent
 and 
Cahouet, Violaine
 and 
Dicko, Ali-Hamadi
 and 
Palombi, Olivier
 and 
Faure, François
 and 
Troccaz, Jocelyne
},
year = {
2014},

publisher = {
The Eurographics Association},


ISSN = {2070-5778},
ISBN = {978-3-905674-62-0},

DOI = {
10.2312/vcbm.20141191}
http://hdl.handle.net/10.2312/vcbm.20141191.191-198}

}

Browse

Recent Submissions

Now showing 1 - 22 of 22
  • Thumbnail Image
    Item
    Robust Cardiac Function Assessment in 4D PC-MRI Data
    (The Eurographics Association, 2014) Köhler, Benjamin; Preim, Uta; Gutberlet, Matthias; Fischbach, Katharina; Preim, Bernhard; Ivan Viola and Katja Buehler and Timo Ropinski
    Four-dimensional phase-contrast magnetic resonance imaging (4D PC-MRI) is a relatively young image modality that allows the non-invasive acquisition of time-resolved, three-dimensional blood flow information. Stroke volumes and regurgitation fractions are two of the main measures to assess the cardiac function and severity of pathologies. The flow volumes in forward and backward direction through a plane inside the vessel are required for their quantification. Unfortunately, the calculations are highly sensitive towards the plane's angulation since orthogonally passing flow is considered. This often leads to physiologically implausible results. In this work, a robust quantification method is introduced to overcome this problem. Collaborating radiologists and cardiologists were carefully observed while estimating stroke volumes in various healthy volunteer and patient datasets with conventional quantification. This facilitated the automatization of their approach which, in turn, allows to derive statistical information about the plane angulation sensitivity. Moreover, the experts expect a continuous decrease of the stroke volume along the vessel course after a peak value above the aortic valve. Conventional methods are often unable to produce this behavior. Thus, we present a procedure to fit a function that ensures such physiologically plausible results. In addition, the technique was adapted for the robust quantification of regurgitation fractions. The performed qualitative evaluation shows the capability of our method to support diagnosis, a parameter evaluation confirms the robustness. Vortex flow was identified as main cause for quantification uncertainties.
  • Thumbnail Image
    Item
    The iCoCooN: Integration of Cobweb Charts with Parallel Coordinates for Visual Analysis of DCE-MRI Modeling Variations
    (The Eurographics Association, 2014) Raidou, Renata G.; Breeuwer, Marcel; Vilanova, Anna; Heide, U. A. van der; Houdt, P. J. van; Ivan Viola and Katja Buehler and Timo Ropinski
    Efficacy of radiotherapy treatment depends on the specific characteristics of tumorous tissues. For the determination of these characteristics, clinical practice uses Dynamic Contrast Enhanced (DCE) Magnetic Resonance Imaging (MRI). DCE-MRI data is acquired and modeled using pharmacokinetic modeling, to derive per voxel a set of parameters, indicative of tissue properties. Different pharmacokinetic modeling approaches make different assumptions, resulting in parameters with different distributions. A priori, it is not known whether there are significant differences between modeling assumptions and which assumption is best to apply. Therefore, clinical researchers need to know at least how different choices in modeling affect the resulting pharmacokinetic parameters and also where parameter variations appear. In this paper, we introduce iCoCooN: a visualization application for the exploration and analysis of model-induced variations in pharmacokinetic parameters.We designed a visual representation, the Cocoon, by integrating perpendicularly Parallel Coordinate Plots (PCPs) with Cobweb Charts (CCs). PCPs display the variations in each parameter between modeling choices, while CCs present the relations in a whole parameter set for each modeling choice. The Cocoon is equipped with interactive features to support the exploration of all data aspects in a single combined view. Additionally, interactive brushing allows to link the observations from the Cocoon to the anatomy. We conducted evaluations with experts and also general users. The clinical experts judged that the Cocoon in combination with its features facilitates the exploration of all significant information and, especially, enables them to find anatomical correspondences. The results of the evaluation with general users indicate that the Cocoon produces more accurate results compared to independent multiples.
  • Thumbnail Image
    Item
    A Survey on Visualizing Magnetic Resonance Spectroscopy Data
    (The Eurographics Association, 2014) Nunes, Miguel; Laruelo, Andrea; Ken, SoleaKhena; Laprie, Anne; Bühler, Katja; Ivan Viola and Katja Buehler and Timo Ropinski
    Data from Magnetic Resonance Spectroscopy Imaging (MRSI) contains signals about biomarkers concentrations, which are used to achieve new knowledge about biochemical processes. These support doctors in identifying and treat diseases as well as better defining regions of interest. In clinical environment, the lack of appropriate methods and tools to visualize MRSI has made this imaging technique information hard to interpret and include in treatment planning workflows. This paper is doing a review on how MRSI data is analysed in a medical environment as well as new approaches from the rendering and visual analytics areas. We conclude that this topic will be under the spotlight in the coming years, as current research is still facing many challenges on which the visualization community can actively contribute to.
  • Thumbnail Image
    Item
    Extracting and Visualizing Uncertainties in Segmentations from 3D Medical Data
    (The Eurographics Association, 2014) Faltin, Peter; Chaisaowong, Kraisorn; Kraus, Thomas; Merhof, Dorit; Ivan Viola and Katja Buehler and Timo Ropinski
    Assessing surfaces of segmentations extracted from 3D image data for medical purposes requires dedicated extraction and visualization methods. In particular, when assessing follow-up cases, the exact volume and confidence level of the segmentation surface is crucial for medical decision-making. This paper introduces a new processing chain comprising a series of carefully selected and well-matched steps to determine and visualize a segmentation boundary. In a first step, the surface, segmentation confidence and statistical partial volume are extracted. Then, a mesh-based method is applied to determine a refined boundary of the segmented object based on these properties, whilst smoothness, confidence of the surface and partial volume are considered locally. In contrast to existing methods, the proposed approach is able to guarantee the estimated volume for the whole segmentation, which is an important prerequisite for clinical application. Furthermore, a novel visualization method is presented which was specifically designed to simultaneously provide information about 3D morphology, confidence and possible errors. As opposed to classical visualization approaches that take advantage of color and transparency but need some geometric mapping and interpretation from the observer, the proposed scattered visualization utilizes density and scattering, which are much closer and more intuitively related to the original geometric meaning. The presented method is particularly suitable to assess pleural thickenings from follow-up CT images, which further illustrates the potential of the proposed method.
  • Thumbnail Image
    Item
    Uncertainty-aware Ensemble of Classifiers for Segmenting Brain MRI Data
    (The Eurographics Association, 2014) Al-Taie, Ahmed; Hahn, Horst K.; Linsen, Lars; Ivan Viola and Katja Buehler and Timo Ropinski
    Estimating and visualizing uncertainty in medical image segmentation has become an active research area due to the necessity of making medical experts aware of possibly wrong segmentation decisions. Still, to our knowledge all these methods are based on a single choice of the underlying segmentation approach. Segmentation using an ensemble of classifiers (or committee machine) use multiple classifiers to increase the performance when compared to applying a single classifier. In this paper, we propose methods to estimate uncertainties in segmentations produced by ensembles of classifiers. We investigate and compare the different combining strategies of the segmentation results of the ensemble members from an uncertainty point of view. We discuss why some combining strategies tend to perform better than others. Also, we visualize the estimated uncertainties using a color mapping in image space and propose a post-segmentations correction step to reclassify the noisy pixels in the final result based on the statistical uncertainty.
  • Thumbnail Image
    Item
    Inlier Detection in Thermal Sensitive Images
    (The Eurographics Association, 2014) Zadicario, Eyal; Carmi, N.; Ju, Tao; Cohen-Or, Daniel; Ivan Viola and Katja Buehler and Timo Ropinski
    Image guidance of medical procedures may use thermal images to monitor a treatment. Analysis of the thermal images by the physician may be time consuming and confusing because the thermal image includes multiple outliers. We present a novel inlier detection method for thermal images that results in reliable thermal information to support medical decision making. Outliers in thermal images are particularly challenging to detect using conventional methods, because they are significantly more abundant than inliers and, like inliers, they may be temporally consistent. Our inlier detection method is physically-based: it is motivated by the fact that heat propagation in soft tissues can be modeled using the bio-heat equation. Pixels are classified as inliers only if the temperature pattern in a spatial and temporal neighborhood strongly correlates with the physical model. For improved robustness, the correlation process includes a 2D filter in the spatial domain and a 3D filter in both spatial and temporal domains. Experiments with real data have shown that our method produces results that agree with annotations provided by human experts even in outlier-laden images. Our results show inliers can be detected leaving true heat pixels for the physician to observe, while not overloading him with the need to analyze outliers. The technique has been integrated in a true clinical environment and is being used to aid physicians in analysis of thermal images
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    Real-Time Dense Nucleus Selection from Confocal Data
    (The Eurographics Association, 2014) Wan, Yong; Otsuna, Hideo; Kwan, K. M.; Hansen, Charles; Ivan Viola and Katja Buehler and Timo Ropinski
    Selecting structures from volume data using direct over-the-visualization interactions, such as a paint brush, is perhaps the most intuitive method in a variety of application scenarios. Unfortunately, it seems difficult to design a universal tool that is effective for all different structures in biology research. In [WOCH12b], an interactive technique was proposed for extracting neural structures from confocal microscopy data. It uses a dual-stroke paint brush to select desired structures directly from volume visualizations. However, the technique breaks down when it was applied to selecting densely packed structures with condensed shapes, such as nuclei from zebrafish eye development research. We collaborated with biologists studying zebrafish eye development and adapted the paint brush tool for real-time nucleus selection from volume data. The morphological diffusion algorithm used in the previous paint brush is restricted to gradient descending directions for improved nucleus boundary definition. Occluded seeds are removed using backward ray-casting. The adapted paint brush is then used in tracking cell movements in a time sequence dataset of a developing zebrafish eye.
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    Imaging the Vascular Network of the Human Spleen from Immunostained Serial Sections
    (The Eurographics Association, 2014) Ulrich, Christine; Lobachev, Oleg; Steiniger, Birte; Guthe, Michael; Ivan Viola and Katja Buehler and Timo Ropinski
    The spleen is one of the organs, where the micro-structure and the function on that level are not completely understood. It was for example only recently found that is has an open circulation, which distinguishes it from all other organs. Imaging the complete vascular network from the arteries to open-ended capillaries would greatly facilitate research in this area. The structure of such tissue is best uncovered using immunehistological staining. This can however only be applied to thin tissue sections and larger structures span several slices. Due to the deformation induced when cutting the specimen, standard registration algorithms cannot be used to merge the images into a volume. We propose a specialized matching algorithm to robustly determine corresponding regions in the images. After a rigid alignment of the scans, we use a cubic B-spline to deform and align the images. During this process we minimize the total deformation to produce as accurate results as possible.
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    Interactive Labeling of Toponome Data
    (The Eurographics Association, 2014) Oeltze-Jafra, Steffen; Pieper, Franz; Hillert, Reyk; Preim, Bernhard; Schubert, Walter; Ivan Viola and Katja Buehler and Timo Ropinski
    Biological multi-channel microscopy data are often characterized by a high local entropy and phenotypically identical structures covering only a few pixels and forming disjoint regions spread over, e.g., a cell or a tissue section. Toponome data as an example, comprise a fluorescence image (channel) per protein affinity reagent, and capture the location and spatial distribution of proteins in cells and tissues. Biologists investigate such data using a region-of-interest in an image view and a linked view displaying information aggregated or derived from the channels. The cognitive effort of moving the attention back and forth between the views is immense. We present an approach for the in-place annotation of multi-channel microscopy data in 2D views. We combine dynamic excentric labeling and static necklace maps to cope with the special characteristics of these data. The generated annotations support the biologists in visually exploring multi-channel information directly in its spatial context. A label is generated per unique phenotype included in a flexible, moveable focus region. The labels are organized in a circular fashion around the focus region. On demand, a nested labeling can be generated by displaying a second ring of labels which represents the channels characterizing the focused phenotypes. We demonstrate our approach by toponome data of a rhabdomyosarcoma cell line and a prostate tissue section.
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    Membrane Mapping: Combining Mesoscopic and Molecular Cell Visualization
    (The Eurographics Association, 2014) Waltemate, Thomas; Sommer, Björn; Botsch, Mario; Ivan Viola and Katja Buehler and Timo Ropinski
    Three-dimensional cell visualization is an important topic in today's cytology-affiliated community. Cell illustrations and animations are used for scientific as well as for educational purposes. Unfortunately, there exist only few tools to support the cell modeling process on a molecular level. A major problem is the immense intracellular size variation between relatively large mesoscopic cell components and small molecular membrane patches. This makes both modeling and visualization of whole cells a challenging task. In this paper we propose Membrane Mapping as an interactive tool for combining the mesoscopic and molecular level. Based on instantly computed local parameterizations we map patches of molecular membrane structures onto user-selected regions of cell components. By designing an efficient and GPU-friendly mapping technique, our approach allows to visualize and map pre-computed molecular dynamics simulations of membrane patches to mesoscopic structures in real-time. This enables the visualization of whole cells on a mesoscopic level with an interactive magnifier tool for inspecting their molecular structure and dynamic behavior.
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    Visualizing Movements of Protein Tunnels in Molecular Dynamics Simulations
    (The Eurographics Association, 2014) Kozlíková, Barbora; Jurcík, Adam; By ka, Jan; Strnad, Ondrej; Sochor, Jirí; Ivan Viola and Katja Buehler and Timo Ropinski
    Analysis and visualization of molecules and their structural features help biochemists and biologists to better understand protein behavior. Studying these structures in molecular dynamics simulations enhances this understanding. In this paper we introduce three approaches for animating specific inner pathways composed of an empty space between atoms, called tunnels. These tunnels facilitate the transport of small molecules, water solvent and ions in many proteins. They help researchers understand the structure-function relationships of proteins and the knowledge of tunnel properties improves the design of new inhibitors. Our methods are derived from selected tunnel representations when each stresses some of the important tunnel properties-width, shape, mapping of physico-chemical properties, etc. Our methods provide smooth animation of the movement of tunnels as they change their length and shape throughout the simulation.
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    Visual and Quantitative Analysis of Higher Order Arborization Overlaps for Neural Circuit Research
    (The Eurographics Association, 2014) Swoboda, Nicolas; Moosburner, Judith; Bruckner, Stefan; Yu, Jai Y.; Dickson, Barry J.; Bühler, Katja; Ivan Viola and Katja Buehler and Timo Ropinski
    Neuroscientists investigate neural circuits in the brain of the common fruit fly Drosophila melanogaster to discover how complex behavior is generated. Hypothesis building on potential connections between individual neurons is an essential step in the discovery of circuits that govern a specific behavior. Overlaps of arborizations of two or more neurons indicate a potential anatomical connection, i.e. the presence of joint synapses responsible for signal transmission between neurons. Obviously, the number of higher order overlaps (i.e. overlaps of three and more arborizations) increases exponentially with the number of neurons under investigation making it almost impossible to precompute quantitative information for all possible combinations. Thus, existing solutions are restricted to pairwise comparison of overlaps as they are relying on precomputed overlap quantification. Analyzing overlaps by visual inspection of more than two arborizations in 2D sections or in 3D is impeded by visual clutter or occlusion. This work contributes a novel tool that complements existing methods for potential connectivity exploration by providing for the first time the possibility to compute and visualize higher order arborization overlaps on the fly and to interactively explore this information in its spatial anatomical context and on a quantitative level. Qualitative evaluation with neuroscientists and non-expert users demonstrated the utility and usability of the tool.
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    Evaluation of Transfer Function Methods in Direct Volume Rendering of the Blood Vessel Lumen
    (The Eurographics Association, 2014) Läthén, Gunnar; Lindholm, Stefan; Lenz, Reiner; Borga, Magnus; Ivan Viola and Katja Buehler and Timo Ropinski
    Visualization of contrast enhanced blood vessels in CT angiography data presents a challenge due to varying concentration of the contrast agent. The purpose of this work is to evaluate the correctness (effectiveness) in visualizing the vessel lumen using two different 3D visualization strategies, thereby assessing the feasibility of using such visualizations for diagnostic decisions. We compare a standard visualization approach with a recent method which locally adapts to the contrast agent concentration. Both methods are evaluated in a parallel setting where the participant is instructed to produce a complete visualization of the vessel lumen, including both large and small vessels, in cases of calcified vessels in the legs. The resulting visualizations are thereafter compared in a slice viewer to assess the correctness of the visualized lumen. The results indicate that the participants generally overestimated the size of the vessel lumen using the standard visualization, whereas the locally adaptive method better conveyed the true anatomy. The participants did find the interpretation of the locally adaptive method to be less intuitive, but also noted that this did not introduce any prohibitive complexity in the work flow. The observed trends indicate that the visualized lumen strongly depends on the width and placement of the applied transfer function and that this dependency is inherently local rather than global. We conclude that methods that permit local adjustments, such as the method investigated in this study, can be beneficial to certain types of visualizations of large vascular trees.
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    Visibility-Driven Processing of Streaming Volume Data
    (The Eurographics Association, 2014) Solteszova, Veronika; Birkeland, Asmund; Viola, Ivan; Bruckner, Stefan; Ivan Viola and Katja Buehler and Timo Ropinski
    In real-time volume data acquisition, such as 4D ultrasound, the raw data is challenging to visualize directly without additional processing. Noise removal and feature detection are common operations, but many methods are too costly to compute over the whole volume when dealing with live streamed data. In this paper, we propose a visibility-driven processing scheme for handling costly on-the-fly processing of volumetric data in real-time. In contrast to the traditional visualization pipeline, our scheme utilizes a fast computation of the potentially visible subset of voxels which significantly reduces the amount of data required to process. As filtering operations modify the data values which may affect their visibility, our method for visibility-mask generation ensures that the set of elements deemed visible does not change after processing. Our approach also exploits the visibility information for the storage of intermediate values when multiple operations are performed in sequence, and can therefore significantly reduce the memory overhead of longer filter pipelines. We provide a thorough technical evaluation of the approach and demonstrate it on several typical scenarios where on-the-fly processing is required.
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    Towards Clinical Deployment of Automated Anatomical Regions-Of-Interest
    (The Eurographics Association, 2014) Lindholm, Stefan; Forsberg, Daniel; Ynnerman, Anders; Knutsson, Hans; Andersson, Mats; Lundström, Claes; Ivan Viola and Katja Buehler and Timo Ropinski
    The purpose of this work is to investigate, and improve, the feasibility of advanced Region Of Interest (ROI) selection schemes in clinical volume rendering. In particular, this work implements and evaluates an Automated Anatomical ROI (AA-ROI) approach based on the combination of automatic image registration (AIR) and Distance- Based Transfer Functions (DBTFs), designed for automatic selection of complex anatomical shapes without relying on prohibitive amounts of interaction. Domain knowledge and clinical experience has been included in the project through participation of practicing radiologists in all phases of the project. This has resulted in a set of requirements that are critical for Direct Volume Rendering applications to be utilized in clinical practice and a prototype AA-ROI implementation that was developed to addresses critical points in existing solutions. The feasibility of the developed approach was assessed through a study where five radiologists investigated three medical data sets with complex ROIs, using both traditional tools and the developed prototype software. Our analysis indicate that advanced, registration based ROI schemes could increase clinical efficiency in time-critical settings for cases with complex ROIs, but also that their clinical feasibility is conditional with respect to the radiologists trust in the registration process and its application to the data.
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    Personalized X-ray Reconstruction of the Proximal Femur via a New Control Point-based 2D-3D Registration and Residual Complexity Minimization
    (The Eurographics Association, 2014) Yu, Weimin; Zheng, Guoyan; Ivan Viola and Katja Buehler and Timo Ropinski
    In this paper we present a new control point-based 2D-3D registration approach for a deformable registration of a 3D volumetric template to a limited number of 2D calibrated C-arm images and show its application to a personalized X-ray reconstruction of the proximal femur. In our approach, the 2D-3D registration is done with a hierarchical two-stage strategy: the scaled rigid 2D-3D registration stage followed by a regularized deformable b-spline 2D-3D registration stage. In both stages, a set of control points with uniform spacing are placed over the domain of the 3D volumetric template first. The registrations are then driven by computing updated positions of these control points with intensity-based 2D-2D image registrations of C-arm images with the associated digitally reconstructed radiographs (DRRs), which then allows computing the associated registration transformation at each stage. In order to account for intensity nonstationarities and complex spatially-varying intensity distortion in the deformable b-spline 2D-3D registration stage, the intensity-based 2D-2D image registrations at this stage are done based on minimizing the complexity of the residual images between the C-arm images and the associated DRRs. Comprehensive experiments on simulated images, on images of cadaveric femurs and on clinical datasets are designed and conducted to evaluate the performance of the proposed approach. Quantitative and qualitative evaluation results are given, which demonstrate the efficacy of the present approach.
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    RegistrationShop: An Interactive 3D Medical Volume Registration System
    (The Eurographics Association, 2014) Smit, Noeska N.; Haneveld, Berend Klein; Staring, Marius; Eisemann, Elmar; Botha, Charl P.; Vilanova, Anna; Ivan Viola and Katja Buehler and Timo Ropinski
    In medical imaging, registration is used to combine images containing information from different modalities or to track treatment effects over time in individual patients. Most registration software packages do not provide an easy-to-use interface that facilitates the use of registration. 2D visualization techniques are often used for visualizing 3D datasets. RegistrationShop was developed to improve and ease the process of volume registration using 3D visualizations and intuitive interactive tools. It supports several basic visualizations of 3D volumetric data. Interactive rigid and non-rigid transformation tools can be used to manipulate the volumes and immediate visual feedback for all rigid transformation tools allows the user to examine the current result in real-time. In this context, we introduce 3D comparative visualization techniques, as well as a way of placing landmarks in 3D volumes. Finally, we evaluated our approach with domain experts, who underlined the potential and usefulness of RegistrationShop.
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    Misalignment Correction in Open Cone-Beam CT
    (The Eurographics Association, 2014) Wieckowski, Adam; Stopp, Fabian; Käseberg, Marc; Keeve, Erwin; Ivan Viola and Katja Buehler and Timo Ropinski
    Cone-beam computed tomography (CBCT) is an established standard for both, medical and industrial volumetric imaging. To compute a 3D volume, multiple 2D x-ray projection images of an object of interest are acquired from different directions. Using the geometric information about the acquisition geometry of each image, the volume is reconstructed. Incorrect geometric information (misalignments) leads to blurring and other artifacts in the resulting reconstruction. The exact acquisition geometry is commonly calculated by the analysis of a scan of a dedicated calibration body (off-line calibration). Such approach requires high repeat accuracy of the scanner mechanics and cannot account for non-systematic deviations. Current methods allowing for misalignment correction without a dedicated phantom, e.g. by iteratively adapting the geometry to minimize the arising artifacts, were developed to work with planar trajectories. It poses a problem for open CBCT systems driving complex trajectories. Therefore, we propose an enhanced method allowing for misalignment correction for general trajectories. We developed a new quality function and a flexible modeling for misalignments. We successfully applied our method to real datasets acquired along planar and non-planar trajectories. The correction with our approach substantially increases the resulting volume quality.
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    Deriving Anatomical Context from 4D Ultrasound
    (The Eurographics Association, 2014) Müller, Markus; Helljesen, Linn E. S.; Prevost, Raphael; Viola, Ivan; Nylund, Kim; Gilja, Odd Helge; Navab, Nassir; Wein, Wolfgang; Ivan Viola and Katja Buehler and Timo Ropinski
    Real-time three-dimensional (also known as 4D) ultrasound imaging using matrix array probes has the potential to create large-volume information of entire organs such as the liver without external tracking hardware. This information can in turn be placed into the context of a CT or MRI scan of the same patient. However for such an approach many image processing challenges need to be overcome and sources of error addressed, including reconstruction drift, anatomical deformations, varying appearance of anatomy, and imaging artifacts. In this work, we present a fully automatic system including robust image-based ultrasound tracking, a novel learning-based global initialization of the anatomical context, and joint mono- and multi-modal registration. In an evaluation on 4D US sequences and MRI scans of eight volunteers we achieve automatic reconstruction and registration without any user interaction, assess the registration errors based on physician-defined landmarks, and demonstrate realtime tracking of free-breathing sequences.
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    A Comparative User Study of a 2D and an Autostereoscopic 3D Display for a Tympanoplastic Surgery
    (The Eurographics Association, 2014) Baer, Alexandra; Huebler, Antje; Saalfeld, Patrick; Cunningham, Douglas; Preim, Bernhard; Ivan Viola and Katja Buehler and Timo Ropinski
    This paper presents the design and execution of a comparative experimental between-participant study with 42 participants. We investigated depth perception comparing a 2D display with a glasses-free 3D autostereoscopic display in detail and conducted a follow-up study with the new 3D zSpace technology including a stylus as input device. This work comprises the design of a tympanoplastic training scenario used as the study's "real world task". Participants had to position a prosthesis implant to reconstruct the ossicular chain and thus a patient's hearing ability. The study revealed an overwhelming support of the 3D autostereoscopic display compared to a 2D display regarding depth judgment, task completion time and the number of required scene and prosthesis interactions.
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    Survey of Labeling Techniques in Medical Visualizations
    (The Eurographics Association, 2014) Oeltze-Jafra, Steffen; Preim, Bernhard; Ivan Viola and Katja Buehler and Timo Ropinski
    Annotations of relevant structures and regions are crucial in diagnostics, treatment planning, medical team meetings as well as in medical education. They serve to focus discussions, present results of collaborative decision making, record and forward diagnostic findings, support orientation in complex or unfamiliar views on the data, and study anatomy. Different techniques have been presented for labeling the original data in 2D slice views, surface representations of structures extracted from the data, e.g., organs and vasculature, and 3D volume rendered representations of the data. All aim at a clear visual association of labels and structures, visible and legible labels, and a fast and aesthetic labeling while considering individual properties of the data and its representation and tackling various issues, e.g., occlusion of structures by labels, overlapping labels, and crossings of lines connecting labels with structures. We survey the medical labeling work and propose a classification with respect to the employed labeling technique. We give guidelines for choosing a technique dependent on the data representation, e.g., surface rendering or slice view, the type of structures to be labeled, and the individual requirements on an effective label layout.
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    Interactive Visualization of Muscle Activity During Limb Movements: Towards Enhanced Anatomy Learning
    (The Eurographics Association, 2014) Bauer, Armelle; Paclet, Florent; Cahouet, Violaine; Dicko, Ali-Hamadi; Palombi, Olivier; Faure, François; Troccaz, Jocelyne; Ivan Viola and Katja Buehler and Timo Ropinski
    We propose a framework to investigate a new way to learn musculoskeletal anatomical kinetics using interactive motion capture and visualization. It can be used to facilitate the learning of anatomy by medicine and sports students, and for the general public to discover human anatomy in action. We illustrate our approach using the example of knee flexion and extension by visualizing the knee muscle activation prediction with agonist and antagonist co-contraction. Muscle activation data for specified movements is first measured during a preliminary phase. The user is then tracked in real time, and its motion is analyzed to recognize the motion being performed. This is used to efficiently evaluate muscle activation by interpolating the activation data stored in tables. The visual feedback consists of a user-specific 3D avatar created by deforming a reference model and animated using the tracking. Muscle activation is visualized using colored lines of action or 3D meshes. This work was made possible by the collaboration of three complementary labs specialized in computer-aided medical intervention, computer graphics and biomechanics.