| 1. |
- Svensson, Lennart, et al.
(författare)
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ProViz : a tool for explorative 3-D visualization and template matching in electron tomograms
- 2017
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Ingår i: Computer Methods in Biomechanics and Biomedical Engineering: Imaging & Visualization. - : Taylor & Francis. - 2168-1163 .- 2168-1171. ; 5:6, s. 446-454
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Tidskriftsartikel (refereegranskat)abstract
- Visual understanding is a key aspect when studying electron tomography data-sets, aside quantitative assessments such as registration of high-resolution structures. We here present the free software tool ProViz (Protein Visualization) for visualisation and template matching in electron tomograms of biological samples. The ProViz software contains methods and tools which we have developed, adapted and computationally optimised for easy and intuitive visualisation and analysis of electron tomograms with low signal-to-noise ratio. ProViz complements existing software in the application field and serves as an easy and convenient tool for a first assessment and screening of the tomograms. It provides enhancements in three areas: (1) improved visualisation that makes connections as well as intensity differences between and within objects or structures easier to see and interpret, (2) interactive transfer function editing with direct visual result feedback using both piecewise linear functions and Gaussian function elements, (3) computationally optimised template matching and tools to visually assess and interactively explore the correlation results. The visualisation capabilities and features of ProViz are demonstrated on various biological volume data-sets: bacterial filament structures in vitro, a desmosome and the transmembrane cadherin connections therein in situ, and liposomes filled with doxorubicin in solution. The explorative template matching is demonstrated on a synthetic IgG data-set.
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| 2. |
- Blache, Ludovic, et al.
(författare)
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SoftCut: : A Virtual Planning Tool for Soft Tissue Resection on CT Images
- 2018
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Ingår i: Medical Image Understanding and Analysis. - Cham : Springer. - 9783319959207 ; , s. 299-310
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Konferensbidrag (refereegranskat)abstract
- With the increasing use of three-dimensional (3D) models and Computer Aided Design (CAD) in the medical domain, virtual surgical planning is now frequently used. Most of the current solutions focus on bone surgical operations. However, for head and neck oncologic resection, soft tissue ablation and reconstruction are common operations. In this paper, we propose a method to provide a fast and efficient estimation of shape and dimensions of soft tissue resections. Our approach takes advantage of a simple sketch-based interface which allows the user to paint the contour of the resection on a patient specific 3D model reconstructed from a computed tomography (CT) scan. The volume is then virtually cut and carved following this pattern. From the outline of the resection defined on the skin surface as a closed curve, we can identify which areas of the skin are inside or outside this shape. We then use distance transforms to identify the soft tissue voxels which are closer from the inside of this shape. Thus, we can propagate the shape of the resection inside the soft tissue layers of the volume. We demonstrate the usefulness of the method on patient specific CT data.
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| 3. |
- Moafi, Roya, et al.
(författare)
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Haptic-Assisted Surgical Planning (HASP) in a Case of Bilateral Mandible Fracture
- 2022
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Ingår i: International Medical Case Reports Journal. - : Dove Medical Press Limited. - 1179-142X. ; 15, s. 707-712
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Tidskriftsartikel (refereegranskat)abstract
- Restoring normal skeletal anatomy in patients with complex trauma to the mandible can be difficult, the difficulty often increasing with an edentulous mandible. This study describes a case of a displaced edentulous bilateral mandibular fracture, which was preoperatively planned with the in-house haptic-assisted surgery planning system (HASP). A model of the virtually restored mandible was 3D-printed at the hospital and a reconstruction plate was outlined beforehand with the printed mandible as a template and served as a guide during surgery. This case suggests HASP as a valuable preoperative tool in the planning phase when dealing with maxillofacial trauma cases. With the application of virtual planning, the authors could analyze the desired outcome and were further supported in surgery by the guidance of the reconstruction plate outlined on the restored model of the mandible.
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| 4. |
- Nilsson, Johanna, et al.
(författare)
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Evaluation of in-house, haptic assisted surgical planning for virtual reduction of complex mandibular fractures
- 2021
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Ingår i: International Journal of Computer Assisted Radiology and Surgery. - : Springer. - 1861-6410 .- 1861-6429. ; 16:6, s. 1059-1068
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Tidskriftsartikel (refereegranskat)abstract
- The management of complex mandible fractures, i.e severely comminuted or fractures of edentulous/atrophic mandibles, can be challenging. This is due to the three-dimensional loss of bone, which limits the possibility for accurate anatomic reduction. Virtual surgery planning (VSP) can provide improved accuracy and shorter operating times, but is often not employed for trauma cases because of time constraints and complex user interfaces limited to two-dimensional interaction with three-dimensional data. In this study, we evaluate the accuracy, precision, and time efficiency of the Haptic Assisted Surgery Planning system (HASP), an in-house VSP system that supports stereo graphics, six degrees-of-freedom input and haptics, to improve the surgical planning. Three operators performed planning in HASP on Computed Tomography (CT) and Come Beam Computed Tomography (CBCT) images of a plastic skull model and on twelve retrospective cases with complex mandible fractures. The result shows an accuracy and reproducibility of less than 2mm when using HASP, with an average planning time of 15 minutes, including time for segmentation in the software BoneSplit. This study presents an in-house haptic assisted planning tool for cranio-maxillofacial surgery with high usability that can be used for preoperative planning and evaluation of complex mandible fractures.
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| 5. |
- Nysjö, Fredrik, 1985-
(författare)
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Clustered Grid Cell Data Structure for Isosurface Rendering
- 2020
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Ingår i: Journal of WSCG. - 1213-6972 .- 1213-6964. ; 28:1-2, s. 9-17
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Tidskriftsartikel (refereegranskat)abstract
- Active grid cells in scalar volume data are typically identified by many isosurface rendering methods when extracting another representation of the data for rendering. However, the use of grid cells themselves as rendering primitives is not extensively explored in the literature. In this paper, we propose a cluster-based data structure for storing the data of active grid cells for fast cell rasterisation via billboard splatting. Compared to previous cell rasterisation approaches, eight corner scalar values are stored with each active grid cell, so that the full volume data is not required during rendering. The grid cells can be quickly extracted and use about 37 percent memory compared to a typical efficient mesh-based representation, while supporting large grid sizes. We present further improvements such as a visibility buffer for cluster culling and EWA-based interpolation of attributes such as normals. We also show that our data structure can be used for hybrid ray tracing or path tracing to compute global illumination.
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| 6. |
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| 7. |
- Nysjö, Fredrik, 1985-
(författare)
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Modeling and Visualization for Virtual Interaction with Medical Image Data
- 2020
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Interactive systems for exploring and analysing medical three dimensional (3D) volume image data using techniques such as stereoscopic rendering and haptics can lead to new workflows for virtual surgery planning. This includes the design of patient-specific surgical guides and plates for additive manufacturing (3D printing). Our applications, medical visualization and cranio-maxillofacial surgery planning, involve large volume data such as computed tomo\-graphy (CT) images with millions of data points. This motivates the development of fast and efficient methods for visualization and haptic rendering, as well as the development of efficient modeling techniques for simplifying the design of 3D printable parts. In this thesis, we develop methods for visualization and haptic rendering of isosurfaces in volume image data, and show applications of these methods to medical visualization and virtual surgery planning. We further develop methods for modeling surgical guides and plates for cranio-maxillofacial surgery, and integrate them into our system for haptics-assisted surgery planning called HASP. This system is now installed at the department of surgical sciences, Uppsala University, and is being evaluated for use in clinical research.
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| 8. |
- Nysjö, Fredrik, 1985-, et al.
(författare)
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RayCaching : Amortized Isosurface Rendering for Virtual Reality
- 2020
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Ingår i: Computer graphics forum (Print). - : Wiley. - 0167-7055 .- 1467-8659. ; 39:1, s. 220-230
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Tidskriftsartikel (refereegranskat)abstract
- Real‐time virtual reality requires efficient rendering methods to deal with high‐ resolution stereoscopic displays and low latency head‐tracking. Our proposed RayCaching method renders isosurfaces of large volume datasets by amortizing raycasting over several frames and caching primary rays as small bricks that can be efficiently rasterized. An occupancy map in form of a clipmap provides level of detail and ensures that only bricks corresponding to visible points on the isosurface are being cached and rendered. Hard shadows and ambient occlusion from secondary rays are also accumulated and stored in the cache. Our method supports real‐time isosurface rendering with dynamic isovalue and allows stereoscopic visualization and exploration of large volume datasets at framerates suitable for virtual reality applications.
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| 9. |
- Nysjö, Fredrik, 1985-, et al.
(författare)
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Signed Distance Fields for Modeling Surgical Guides and Plates from CT Images
- 2016
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Ingår i: Proc, Swedish Symposium on Image Analysis.
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- User-friendly virtual surgery planning(VSP) systems for reconstructive surgery, such as cranio-maxillofacial (CMF) surgery, that can be used by the surgeons themselves without help of a technician have the potential to shorten the pre-operative planning from days to hours. An important part of such systems is the design of surgical guides and plates for osteosynthesis. We describe a method for generating surgical guide and plate models from computed tomography (CT) images, using signed distance fields and constructive solidgeometry (CSG). We implement the method as an extension to our Haptics-Assisted Surgery Plan-ning (HASP) system that enables a user to quickly design guide and plate models with stereo graphics and haptic feedback. We find that surgical guide and plate models can be efficiently generated from segmented CT images with our method. We also find that an anti-aliased distance transform can improve the accuracy and precision of the modelingin this application.
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| 10. |
- Nysjö, Fredrik, 1985-, et al.
(författare)
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Vectorised High-Fidelity Haptic Rendering with Dynamic Pointshell
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Exploiting parallelism in haptic rendering algorithms for rigid body collision simulation can be difficult due to the haptic feedback loop imposing strict real-time constraints on the computations. In this paper, we show that the classical Voxmap PointShell algorithm can be efficiently vectorised via the single-program multiple-data (SPMD) programming model of the Intel SPMD Program Compiler (ISPC) compiler and programming language. Our vectorised version provides an average 3.0x speedup compared to a corresponding scalar implementation, for a static hierarchical pointshell on a single CPU core. In addition, we propose a dynamic pointshell that does not require any pre-processing and allows a fixed point budget to be set per frame. The speedup obtained by the vectorisation means that a larger number of contact queries can be processed per haptic frame, while maintaining a desired haptic framerate. In an empirical study, we demonstrate that this increased fidelity in collision simulation translates directly to a higher user accuracy in assembly of fractured virtual objects.
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| 11. |
- Pielawski, Nicolas, et al.
(författare)
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TissUUmaps 3 : Improvements in interactive visualization, exploration, and quality assessment of large-scale spatial omics data
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Background and Objectives: Spatially resolved techniques for exploring the molecular landscape of tissue samples, such as spatial transcriptomics, often result in millions of data points and images too large to view on a regular desktop computer, limiting the possibilities in visual interactive data exploration. TissUUmaps is a free, open-source browser-based tool for GPU-accelerated visualization and interactive exploration of 107+ data points overlaying tissue samples.Methods: Herein we describe how TissUUmaps 3 provides instant multiresolution image viewing and can be customized, shared, and also integrated into Jupyter Notebooks. We introduce new modules where users can visualize markers and regions, explore spatial statistics, perform quantitative analyses of tissue morphology, and assess the quality of decoding in situ transcriptomics data.Results: We show that thanks to targeted optimizations the time and cost associated with interactive data exploration were reduced, enabling TissUUmaps 3 to handle the scale of today’s spatial transcriptomics methods.Conclusion: TissUUmaps 3 provides significantly improved performance for large multiplex datasets as compared to previous versions. We envision TissUUmaps to contribute to broader dissemination and flexible sharing of large-scale spatial omics data.
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| 12. |
- Pielawski, Nicolas, et al.
(författare)
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TissUUmaps 3 : Improvements in interactive visualization, exploration, and quality assessment of large-scale spatial omics data
- 2023
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Ingår i: Heliyon. - : Elsevier BV. - 2405-8440. ; 9:5
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Tidskriftsartikel (refereegranskat)abstract
- Background and objectives: Spatially resolved techniques for exploring the molecular landscape of tissue samples, such as spatial transcriptomics, often result in millions of data points and images too large to view on a regular desktop computer, limiting the possibilities in visual interactive data exploration. TissUUmaps is a free, open-source browser-based tool for GPU-accelerated visualization and interactive exploration of 107+ data points overlaying tissue samples.Methods: Herein we describe how TissUUmaps 3 provides instant multiresolution image viewing and can be customized, shared, and also integrated into Jupyter Notebooks. We introduce new modules where users can visualize markers and regions, explore spatial statistics, perform quantitative analyses of tissue morphology, and assess the quality of decoding in situ transcriptomics data.Results: We show that thanks to targeted optimizations the time and cost associated with interactive data exploration were reduced, enabling TissUUmaps 3 to handle the scale of today's spatial transcriptomics methods.Conclusion: TissUUmaps 3 provides significantly improved performance for large multiplex datasets as compared to previous versions. We envision TissUUmaps to contribute to broader dissemination and flexible sharing of largescale spatial omics data.
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