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Lindholm, Stefan
Publications (10 of 14) Show all publications
Lindholm, S., Jönsson, D., Hansen, C. & Ynnerman, A. (2014). Boundary Aware Reconstruction of Scalar Fields. IEEE Transactions on Visualization and Computer Graphics, 20(12), 2447-2455.
Open this publication in new window or tab >>Boundary Aware Reconstruction of Scalar Fields
2014 (English)In: IEEE Transactions on Visualization and Computer Graphics, ISSN 1077-2626, E-ISSN 1941-0506, Vol. 20, no 12, 2447-2455 p.Article in journal (Refereed) Published
Abstract [en]

In visualization, the combined role of data reconstruction and its classification plays a crucial role. In this paper we propose a novel approach that improves classification of different materials and their boundaries by combining information from the classifiers at the reconstruction stage. Our approach estimates the targeted materials’ local support before performing multiple material-specific reconstructions that prevent much of the misclassification traditionally associated with transitional regions and transfer function (TF) design. With respect to previously published methods our approach offers a number of improvements and advantages. For one, it does not rely on TFs acting on derivative expressions, therefore it is less sensitive to noisy data and the classification of a single material does not depend on specialized TF widgets or specifying regions in a multidimensional TF. Additionally, improved classification is attained without increasing TF dimensionality, which promotes scalability to multivariate data. These aspects are also key in maintaining low interaction complexity. The results are simple-to-achieve visualizations that better comply with the user’s understanding of discrete features within the studied object.

Place, publisher, year, edition, pages
IEEE Press, 2014
National Category
Computer and Information Sciences Computer Sciences
Identifiers
urn:nbn:se:liu:diva-110227 (URN)10.1109/TVCG.2014.2346351 (DOI)000344991700090 ()
Available from: 2014-09-04 Created: 2014-09-04 Last updated: 2018-01-11Bibliographically approved
Läthén, G., Lindholm, S., Lenz, R. & Borga, M. (2014). Evaluation of transfer function methods in direct volume rendering of the blood vessel lumen. In: Ivan Viola and Katja Buehler and Timo Ropinski (Ed.), Proceedings from the EG VCBM 2014. Eurographics Workshop on Visual Computing for Biology and Medicine, Vienna, Austria, September 4–5, 2014: . Paper presented at EG VCBM 2014. Eurographics Workshop on Visual Computing for Biology and Medicine, Vienna, Austria, September 4–5, 2014 (pp. 117-126). Eurographics - European Association for Computer Graphics.
Open this publication in new window or tab >>Evaluation of transfer function methods in direct volume rendering of the blood vessel lumen
2014 (English)In: Proceedings from the EG VCBM 2014. Eurographics Workshop on Visual Computing for Biology and Medicine, Vienna, Austria, September 4–5, 2014 / [ed] Ivan Viola and Katja Buehler and Timo Ropinski, Eurographics - European Association for Computer Graphics, 2014, 117-126 p.Conference paper, Published paper (Refereed)
Abstract [en]

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

Place, publisher, year, edition, pages
Eurographics - European Association for Computer Graphics, 2014
Series
Eurographics Workshop on Visual Computing for Biology and Medicine, ISSN 2070-5778
National Category
Medical Image Processing
Identifiers
urn:nbn:se:liu:diva-97370 (URN)10.2312/vcbm.20141197 (DOI)978-3-905674-62-0 (ISBN)
Conference
EG VCBM 2014. Eurographics Workshop on Visual Computing for Biology and Medicine, Vienna, Austria, September 4–5, 2014
Available from: 2013-09-10 Created: 2013-09-10 Last updated: 2016-08-31Bibliographically approved
Lindholm, S., Falk, M., Sundén, E., Bock, A., Ynnerman, A. & Ropinski, T. (2014). Hybrid Data Visualization Based On Depth Complexity Histogram Analysis. Computer graphics forum (Print), 34(1), 74-85.
Open this publication in new window or tab >>Hybrid Data Visualization Based On Depth Complexity Histogram Analysis
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2014 (English)In: Computer graphics forum (Print), ISSN 0167-7055, E-ISSN 1467-8659, Vol. 34, no 1, 74-85 p.Article in journal (Refereed) Published
Abstract [en]

In many cases, only the combination of geometric and volumetric data sets is able to describe a single phenomenon under observation when visualizing large and complex data. When semi-transparent geometry is present, correct rendering results require sorting of transparent structures. Additional complexity is introduced as the contributions from volumetric data have to be partitioned according to the geometric objects in the scene. The A-buffer, an enhanced framebuffer with additional per-pixel information, has previously been introduced to deal with the complexity caused by transparent objects. In this paper, we present an optimized rendering algorithm for hybrid volume-geometry data based on the A-buffer concept. We propose two novel components for modern GPUs that tailor memory utilization to the depth complexity of individual pixels. The proposed components are compatible with modern A-buffer implementations and yield performance gains of up to eight times compared to existing approaches through reduced allocation and reuse of fast cache memory. We demonstrate the applicability of our approach and its performance with several examples from molecular biology, space weather, and medical visualization containing both, volumetric data and geometric structures.

Place, publisher, year, edition, pages
John Wiley & Sons, 2014
National Category
Computer and Information Sciences Computer Sciences
Identifiers
urn:nbn:se:liu:diva-110238 (URN)10.1111/cgf.12460 (DOI)000350145600008 ()
Note

On the day of the defence date the status of this publication was Manuscript.

Available from: 2014-09-04 Created: 2014-09-04 Last updated: 2018-01-11Bibliographically approved
Lindholm, S. (2014). Medical Volume Visualization Beyond Single Voxel Values. (Doctoral dissertation). Linköping: Linköping University Electronic Press.
Open this publication in new window or tab >>Medical Volume Visualization Beyond Single Voxel Values
2014 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Medical visualization involves many complex decisions for both the user and the imaging algorithms. This thesis aims to improve medical volume visualization through a series of technical contributions to aid such decision processes. Improvements are achieved by using more data, beyond single voxels, in the associated visual analyses.

Simultaneous visualization of multiple data sources and different data formats is rapidly becoming a necessity. This is due to both the growing number of data producing image acquisition techniques as well as the increase in geometric data representations that can be created. Maintaining high rendering performance under these circumstances is challenging, but necessary, to support an exploratory visualization process. This thesis proposes two algorithms to address this challenge: a multi-volume approach that applies binary-space partitioning to solve painters' algorithm geometrically and a rendering algorithm for hybrid data that improves the management of the available graphics memory.

Additional information for decision support is often derived from the captured image data. Classification techniques, in particular, often utilize secondary information sources or neighborhood analysis as means to improve specificity. One example is a proposed algorithm that improves visualization of blood vessels by automatically optimizing visualization parameters based on observed vesselness. This thesis also proposes algorithms involving neighborhood analysis, with a particular focus on domain specific classification knowledge provided by the user. One algorithm provides the ability to semantically state spatial relations between tissues based on encoded material information. Another algorithm improves the representation of discrete features by integrating the users' knowledge in the reconstruction step of the visualization pipeline.

Many of the methods proposed in this thesis can also be applied to other domains, but are all described here in the context of medical volume visualization as most of the research has been performed within this field.

Place, publisher, year, edition, pages
Linköping: Linköping University Electronic Press, 2014. 79 p.
Series
Linköping Studies in Science and Technology. Dissertations, ISSN 0345-7524 ; 1614
National Category
Computer and Information Sciences Computer Sciences Medical Image Processing
Identifiers
urn:nbn:se:liu:diva-110239 (URN)10.3384/diss.diva-110239 (DOI)978-91-7519-256-7 (ISBN)
Public defence
2014-10-03, Domteatern, Visualiseringscenter C, Kungsgatan 54, Norrköping, 09:00 (English)
Opponent
Supervisors
Available from: 2014-09-04 Created: 2014-09-04 Last updated: 2018-01-11Bibliographically approved
Lindholm, S., Forsberg, D., Ynnerman, A., Knutsson, H., Andersson, M. & Lundström, C. (2014). Towards Clinical Deployment of Automated Anatomical Regions-Of-Interest. In: I. Viola, K. Bühler, and T. Ropinski (Ed.), Ivan Viola and Katja Buehler and Timo Ropinski (Ed.), Eurographics Workshop on Visual Computing for Biology and Medicine: . Paper presented at VCBM 2014 : Eurographics Workshop on Visual Computing for Biology and Medicine, September 4-5, Vienna, Austira (pp. 137-143). Eurographics - European Association for Computer Graphics.
Open this publication in new window or tab >>Towards Clinical Deployment of Automated Anatomical Regions-Of-Interest
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2014 (English)In: Eurographics Workshop on Visual Computing for Biology and Medicine / [ed] Ivan Viola and Katja Buehler and Timo Ropinski, Eurographics - European Association for Computer Graphics, 2014, 137-143 p.Conference paper, Published paper (Refereed)
Abstract [en]

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.

Place, publisher, year, edition, pages
Eurographics - European Association for Computer Graphics, 2014
Series
Eurographics Workshop on Visual Computing for Biology and Medicine, ISSN 2070-5778
National Category
Computer and Information Sciences Computer Sciences
Identifiers
urn:nbn:se:liu:diva-110233 (URN)10.2312/vcbm.20141199 (DOI)978-3-905674-62-0 (ISBN)
Conference
VCBM 2014 : Eurographics Workshop on Visual Computing for Biology and Medicine, September 4-5, Vienna, Austira
Available from: 2014-09-04 Created: 2014-09-04 Last updated: 2018-01-11Bibliographically approved
Lindholm, S. & Bock, A. (2013). Poor Man’s Rendering Of Segmented Data. In: Timo Ropinski and Jonas Unger (Ed.), Proceedings of SIGRAD 2013; Visual Computing: . Paper presented at SIGRAD 2013, Norrköping, Sweden, 13-14 June 2013 (pp. 49-54). Linköping University Electronic Press.
Open this publication in new window or tab >>Poor Man’s Rendering Of Segmented Data
2013 (English)In: Proceedings of SIGRAD 2013; Visual Computing / [ed] Timo Ropinski and Jonas Unger, Linköping University Electronic Press, 2013, 49-54 p.Conference paper, Published paper (Refereed)
Abstract [en]

In this paper we present a set of techniques for fast and efficient rendering of segmented data. Our approach utilizes the expected difference between two co-located texture lookups of a label volume, taken with different interpolation filters, as a feature boundary indicator. This allows us to achieve smooth class boundaries without needing to explicitly sample all eight neighbors in the label volume as is the case with previous methods. We also present a data encoding scheme that greatly simplifies transfer function construction.

Place, publisher, year, edition, pages
Linköping University Electronic Press, 2013
Series
Linköping Electronic Conference Proceedings, ISSN 1650-3686 (print), 1650-3740 (online) ; 094
National Category
Computer Vision and Robotics (Autonomous Systems)
Identifiers
urn:nbn:se:liu:diva-96043 (URN)978-91-7519-455-4 (ISBN)
Conference
SIGRAD 2013, Norrköping, Sweden, 13-14 June 2013
Projects
CADICS, CMIV
Available from: 2013-08-14 Created: 2013-08-14 Last updated: 2018-01-11Bibliographically approved
Lindholm, S., Jönsson, D., Knutsson, H. & Ynnerman, A. (2013). Towards Data Centric Sampling for Volume Rendering. In: T. Ropinski and J. Unger (Ed.), SIGRAD 2013: . Paper presented at SIGRAD 2013, 13-14 June 2013, Norrköping, Sweden (pp. 55-60). Linköping University Electronic Press.
Open this publication in new window or tab >>Towards Data Centric Sampling for Volume Rendering
2013 (English)In: SIGRAD 2013 / [ed] T. Ropinski and J. Unger, Linköping University Electronic Press , 2013, 55-60 p.Conference paper, Published paper (Refereed)
Abstract [en]

We present a new method for sampling the volume rendering integral in volume raycasting where samples are correlated based on transfer function content and data set values. This has two major advantages. First, visual artifacts stemming from structured noise, such as wood grain, can be reduced. Second, we will show that the volume data does not longer need to be available during the rendering phase; a surface representation is used instead, which opens up ample oppurtinities for rendering of large data. We will show that the proposed sampling method gives higher quality renderings with fewer samples when compared to regular sampling in the spatial domain.

Place, publisher, year, edition, pages
Linköping University Electronic Press, 2013
Series
Linköping Electronic Conference Proceedings, ISSN 1650-3686 (print), 1650-3740 (online)
National Category
Electrical Engineering, Electronic Engineering, Information Engineering
Identifiers
urn:nbn:se:liu:diva-95674 (URN)978-91-7519-455-4 (ISBN)
Conference
SIGRAD 2013, 13-14 June 2013, Norrköping, Sweden
Projects
CADICSCMIV
Funder
Linnaeus research environment CADICS
Available from: 2013-07-16 Created: 2013-07-16 Last updated: 2015-09-23Bibliographically approved
Läthén, G., Lindholm, S., Lenz, R., Persson, A. & Borga, M. (2012). Automatic Tuning of Spatially Varying Transfer Functions for Blood Vessel Visualization. Paper presented at SciVis. IEEE Transactions on Visualization and Computer Graphics, 18(12), 2345-2354.
Open this publication in new window or tab >>Automatic Tuning of Spatially Varying Transfer Functions for Blood Vessel Visualization
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2012 (English)In: IEEE Transactions on Visualization and Computer Graphics, ISSN 1077-2626, E-ISSN 1941-0506, Vol. 18, no 12, 2345-2354 p.Article in journal (Refereed) Published
Abstract [en]

Computed Tomography Angiography (CTA) is commonly used in clinical routine for diagnosing vascular diseases. The procedure involves the injection of a contrast agent into the blood stream to increase the contrast between the blood vessels and the surrounding tissue in the image data. CTA is often visualized with Direct Volume Rendering (DVR) where the enhanced image contrast is important for the construction of Transfer Functions (TFs). For increased efficiency, clinical routine heavily relies on preset TFs to simplify the creation of such visualizations for a physician. In practice, however, TF presets often do not yield optimal images due to variations in mixture concentration of contrast agent in the blood stream. In this paper we propose an automatic, optimization- based method that shifts TF presets to account for general deviations and local variations of the intensity of contrast enhanced blood vessels. Some of the advantages of this method are the following. It computationally automates large parts of a process that is currently performed manually. It performs the TF shift locally and can thus optimize larger portions of the image than is possible with manual interaction. The method is based on a well known vesselness descriptor in the definition of the optimization criterion. The performance of the method is illustrated by clinically relevant CT angiography datasets displaying both improved structural overviews of vessel trees and improved adaption to local variations of contrast concentration. 

Place, publisher, year, edition, pages
IEEE, 2012
National Category
Radiology, Nuclear Medicine and Medical Imaging Medical Image Processing
Identifiers
urn:nbn:se:liu:diva-79365 (URN)10.1109/TVCG.2012.203 (DOI)000310143100038 ()
Conference
SciVis
Available from: 2012-07-15 Created: 2012-07-15 Last updated: 2017-12-07Bibliographically approved
Lundström, C., Persson, A., Ross, S., Ljung, P., Lindholm, S., Gyllensvärd, F. & Ynnerman, A. (2012). State-of-the-art of visualization in post-mortem imaging. Acta Pathologica, Microbiologica et Immunologica Scandinavica (APMIS), 120(4), 316-326.
Open this publication in new window or tab >>State-of-the-art of visualization in post-mortem imaging
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2012 (English)In: Acta Pathologica, Microbiologica et Immunologica Scandinavica (APMIS), ISSN 0903-4641, E-ISSN 1600-0463, Vol. 120, no 4, 316-326 p.Article, review/survey (Refereed) Published
Abstract [en]

Autopsies constitute a valuable feedback to the healthcare chain to achieve improvements in quality of care and cost effectiveness. This review describes post-mortem imaging, which has emerged as an important part of the pathology toolbox. A broad range of visualization aspects within post-mortem imaging are covered. General state-of-the-art overviews of the components in the visualization pipeline are complemented by in-depth descriptions of methods developed by the authors and our collaborators. The forensic field is represented and related to, as it is spearheading much development in postmortem imaging. Other topics are workflow, imaging data acquisition, and visualization rendering technology. All in all, this review shows the mature state of visual analysis for a non-or minimal-invasive investigation of the deceased patient.

Place, publisher, year, edition, pages
Wiley-Blackwell, 2012
Keyword
Post-mortem imaging, visualization, computed tomography, magnetic resonance imaging, volume rendering
National Category
Engineering and Technology
Identifiers
urn:nbn:se:liu:diva-76806 (URN)10.1111/j.1600-0463.2011.02857.x (DOI)000301656000007 ()
Available from: 2012-04-20 Created: 2012-04-20 Last updated: 2017-12-07
Lindholm, S. & Kronander, J. (2011). Accounting for Uncertainty in Medical Data: A CUDA Implementation of Normalized Convolution. In: Evaluations of graphics and visualization - efficiency, usefulness, accessibility, usability.. Paper presented at SIGRAD 2011, 17–18 November, Stockholm. .
Open this publication in new window or tab >>Accounting for Uncertainty in Medical Data: A CUDA Implementation of Normalized Convolution
2011 (English)In: Evaluations of graphics and visualization - efficiency, usefulness, accessibility, usability., 2011Conference paper, Published paper (Refereed)
Abstract [en]

The domain of medical imaging is naturally moving towards methods that can represent, and account for, localuncertainties in the image data. Even so, fast and efficient solutions that take uncertainty into account are notreadily available even for common problems such as gradient estimation. In this work we present a CUDA imple-mentation of Normalized Convolution, an uncertainty-aware image processing technique, well established in thesignal processing domain. Our results show that up to 100X speedups are possible, which enables full resolutionCT images to be processed at interactive processing speeds, fulfilling demands of both efficiency and interactivitythat exist in the medical domain.

National Category
Engineering and Technology
Identifiers
urn:nbn:se:liu:diva-78337 (URN)
Conference
SIGRAD 2011, 17–18 November, Stockholm
Available from: 2012-06-09 Created: 2012-06-09 Last updated: 2012-06-29
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