uu.seUppsala University Publications
Change search
Link to record
Permanent link

Direct link
BETA
Nysjö, Fredrik
Publications (10 of 15) Show all publications
Nysjö, F. (2020). Modeling and Visualization for Virtual Interaction with Medical Image Data. (Doctoral dissertation). Uppsala: Acta Universitatis Upsaliensis
Open this publication in new window or tab >>Modeling and Visualization for Virtual Interaction with Medical Image Data
2020 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

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.

Place, publisher, year, edition, pages
Uppsala: Acta Universitatis Upsaliensis, 2020. p. 50
Series
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology, ISSN 1651-6214 ; 1898
Keywords
medical image processing, volume rendering, haptic rendering, medical visualization, virtual surgery planning
National Category
Computer Sciences Medical Image Processing
Research subject
Computerized Image Processing
Identifiers
urn:nbn:se:uu:diva-403104 (URN)978-91-513-0864-7 (ISBN)
Public defence
2020-03-13, ITC 2446, Lägerhyddsvägen 2, Hus 2, Polacksbacken, Uppsala, 10:15 (English)
Opponent
Supervisors
Available from: 2020-02-19 Created: 2020-01-23 Last updated: 2020-02-19
Nysjö, F., Malmberg, F. & Nyström, I. (2019). RayCaching: Amortized Isosurface Rendering for Virtual Reality. Computer graphics forum (Print)
Open this publication in new window or tab >>RayCaching: Amortized Isosurface Rendering for Virtual Reality
2019 (English)In: Computer graphics forum (Print), ISSN 0167-7055, E-ISSN 1467-8659Article in journal (Refereed) Epub ahead of print
Abstract [en]

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.

Place, publisher, year, edition, pages
John Wiley & Sons, 2019
Keywords
ray tracing, visibility, point-based models, virtual reality
National Category
Computer Sciences
Research subject
Computerized Image Processing
Identifiers
urn:nbn:se:uu:diva-398397 (URN)10.1111/cgf.13762 (DOI)
Available from: 2019-12-05 Created: 2019-12-05 Last updated: 2020-01-23Bibliographically approved
Blache, L., Nysjö, F., Malmberg, F., Thor, A., Rodriguez-Lorenzo, A. & Nyström, I. (2018). SoftCut:: A Virtual Planning Tool for Soft Tissue Resection on CT Images. In: Mark Nixon; Sasan Mahmoodi; Reyer Zwiggelaar (Ed.), Medical Image Understanding and Analysis: . Paper presented at 22nd Medical Image Understanding and Analysis (MIUA), Southampton, UK, 2018 (pp. 299-310). Cham: Springer, 894
Open this publication in new window or tab >>SoftCut:: A Virtual Planning Tool for Soft Tissue Resection on CT Images
Show others...
2018 (English)In: Medical Image Understanding and Analysis / [ed] Mark Nixon; Sasan Mahmoodi; Reyer Zwiggelaar, Cham: Springer, 2018, Vol. 894, p. 299-310Conference paper, Published paper (Refereed)
Abstract [en]

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.

Place, publisher, year, edition, pages
Cham: Springer, 2018
Series
Communications in Computer and Information Science
National Category
Medical Image Processing
Research subject
Computerized Image Processing
Identifiers
urn:nbn:se:uu:diva-364351 (URN)10.1007/978-3-319-95921-4_28 (DOI)978-3-319-95920-7 (ISBN)
Conference
22nd Medical Image Understanding and Analysis (MIUA), Southampton, UK, 2018
Available from: 2018-10-25 Created: 2018-10-25 Last updated: 2019-03-14Bibliographically approved
Svensson, L., Svensson, S., Nyström, I., Nysjö, F., Nysjö, J., Laloeuf, A., . . . Sintorn, I.-M. (2017). ProViz: a tool for explorative 3-D visualization and template matching in electron tomograms. COMPUTER METHODS IN BIOMECHANICS AND BIOMEDICAL ENGINEERING-IMAGING AND VISUALIZATION, 5(6), 446-454
Open this publication in new window or tab >>ProViz: a tool for explorative 3-D visualization and template matching in electron tomograms
Show others...
2017 (English)In: COMPUTER METHODS IN BIOMECHANICS AND BIOMEDICAL ENGINEERING-IMAGING AND VISUALIZATION, ISSN 2168-1163, Vol. 5, no 6, p. 446-454Article in journal (Refereed) Published
Abstract [en]

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 templatematching 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.

Keywords
Electron tomography, direct volume rendering, image registration, connected component filtering, visualisation and analysis software
National Category
Bioinformatics (Computational Biology)
Identifiers
urn:nbn:se:uu:diva-359635 (URN)10.1080/21681163.2016.1154483 (DOI)000428130400009 ()
Funder
Swedish Foundation for Strategic Research VINNOVA
Available from: 2018-09-05 Created: 2018-09-05 Last updated: 2018-09-05Bibliographically approved
Nysjö, F., Olsson, P., Malmberg, F., Carlbom, I. B. & Nyström, I. (2017). Using anti-aliased signed distance fields for generating surgical guides and plates from CT images. Journal of WSCG, 25(1), 11-20
Open this publication in new window or tab >>Using anti-aliased signed distance fields for generating surgical guides and plates from CT images
Show others...
2017 (English)In: Journal of WSCG, ISSN 1213-6972, E-ISSN 1213-6964, Vol. 25, no 1, p. 11-20Article in journal (Refereed) Published
National Category
Medical Image Processing
Research subject
Computerized Image Processing
Identifiers
urn:nbn:se:uu:diva-335346 (URN)
Available from: 2017-12-04 Created: 2017-12-04 Last updated: 2020-01-23Bibliographically approved
Olsson, P., Nysjö, F., Carlbom, I. B. & Johansson, S. (2016). Comparison of walking and traveling-wave piezoelectric motors as actuators in kinesthetic haptic devices. IEEE Transactions on Haptics, 9(3), 427-431
Open this publication in new window or tab >>Comparison of walking and traveling-wave piezoelectric motors as actuators in kinesthetic haptic devices
2016 (English)In: IEEE Transactions on Haptics, ISSN 1939-1412, E-ISSN 2329-4051, Vol. 9, no 3, p. 427-431Article in journal (Refereed) Published
Abstract [en]

Piezoelectric motors offer an attractive alternative to electromagnetic actuators in portable haptic interfaces: they are compact, have a high force-to-volume ratio, and can operate with limited or no gearing. However, the choice of a piezoelectric motor type is not obvious due to differences in performance characteristics. We present our evaluation of two commercial, operationally different, piezoelectric motors acting as actuators in two kinesthetic haptic grippers, a walking quasi-static motor and a traveling wave ultrasonic motor. We evaluate each gripper's ability to display common virtual objects including springs, dampers, and rigid walls, and conclude that the walking quasi-static motor is superior at low velocities. However, for applications where high velocity is required, traveling wave ultrasonic motors are a better option.

National Category
Human Computer Interaction Robotics
Research subject
Computerized Image Processing; Engineering Science with specialization in Microsystems Technology
Identifiers
urn:nbn:se:uu:diva-262371 (URN)10.1109/TOH.2016.2537803 (DOI)000384670000012 ()27046907 (PubMedID)
Funder
Vårdal FoundationVINNOVA
Available from: 2016-03-30 Created: 2015-09-14 Last updated: 2018-01-11Bibliographically approved
Nysjö, F., Olsson, P., Malmberg, F., Carlbom, I. B. & Nyström, I. (2016). Signed Distance Fields for Modeling Surgical Guides and Plates from CT Images. In: Proc, Swedish Symposium on Image Analysis: SSBA 2016. Paper presented at SSBA 2016.
Open this publication in new window or tab >>Signed Distance Fields for Modeling Surgical Guides and Plates from CT Images
Show others...
2016 (English)In: Proc, Swedish Symposium on Image Analysis: SSBA 2016, 2016Conference paper, Published paper (Other academic)
Abstract [en]

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.

Keywords
3D modeling, patient-specific implants, CT, signed distance fields, constructive solid geometry
National Category
Medical Image Processing
Research subject
Computerized Image Processing
Identifiers
urn:nbn:se:uu:diva-309767 (URN)
Conference
SSBA 2016
Available from: 2016-12-07 Created: 2016-12-07 Last updated: 2016-12-21
Nyström, I., Olsson, P., Nysjö, J., Nysjö, F., Malmberg, F., Seipel, S., . . . Carlbom, I. B. (2016). Virtual Cranio-Maxillofacial Surgery Planning with Stereo Graphics and Haptics. In: Ritacco, Lucas E., Milano, Federico E., Chao, Edmund (Ed.), Computer-Assisted Musculoskeletal Surgery: Thinking and Executing in 3D (pp. 29-42). Springer International Publishing
Open this publication in new window or tab >>Virtual Cranio-Maxillofacial Surgery Planning with Stereo Graphics and Haptics
Show others...
2016 (English)In: Computer-Assisted Musculoskeletal Surgery: Thinking and Executing in 3D / [ed] Ritacco, Lucas E., Milano, Federico E., Chao, Edmund, Springer International Publishing , 2016, p. 29-42Chapter in book (Refereed)
Abstract [en]

Computer-Assisted Surgery (CAS) is a new tool for performing complex procedures in a predictable and safe way. This book is designed to serve as a comprehensive review of Computer-Assisted Surgery, covering the current status of both research and applications.

CAS includes Virtual Preoperative Planning (VPP) and Intraoperative Virtual Navigation (IVN), which are a set of technologies used to measure oncological margins in 3-Dimensions (3D), to locate small intraosseous tumors and apply controlled resections preserving anatomical structures. During VPP, patient acquired multimodal images are processed and an interactive virtual scenario is created. This can then be used as a  platform to  measure oncological distances and preplan osteotomies in safe areas. IVN is a procedure which allows the execution of the VPP with a mean error of less than 3mm.

For the student, medical doctors, research and development scientists or new researchers, the protocols are central to the performance of Computer-Assisted technologies.  

Place, publisher, year, edition, pages
Springer International Publishing, 2016
National Category
Medical and Health Sciences
Identifiers
urn:nbn:se:uu:diva-268677 (URN)10.1007/978-3-319-12943-3 (DOI)978-319-12942-6 (ISBN)978-3-319-12943-3 (ISBN)
Available from: 2015-12-09 Created: 2015-12-09 Last updated: 2016-01-19
Olsson, P., Nysjö, F., Rodríguez-Lorenzo, A., Thor, A., Hirsch, J.-M. & Carlbom, I. B. (2015). Haptics-assisted Virtual Planning of Bone, Soft Tissue, and Vessels in Fibula Osteocutaneous Free Flaps. Plastic and Reconstructive Surgery - Global Open, 3(8), Article ID e479.
Open this publication in new window or tab >>Haptics-assisted Virtual Planning of Bone, Soft Tissue, and Vessels in Fibula Osteocutaneous Free Flaps
Show others...
2015 (English)In: Plastic and Reconstructive Surgery - Global Open, ISSN 2169-7574, Vol. 3, no 8, article id e479Article in journal (Refereed) Published
Abstract [en]

Background: Virtual surgery planning has proven useful for reconstructing head and neck defects by fibula osteocutaneous free flaps (FOFF). Benefits include improved healing, function, and aesthetics, as well as cost savings. But available virtual surgery planning systems incorporating fibula in craniomaxillofacial reconstruction simulate only bone reconstruction without considering vessels and soft tissue.

Methods: The Haptics-Assisted Surgery Planning (HASP) system incorporates bone, vessels, and soft tissue of the FOFF in craniomaxillofacial defect reconstruction. Two surgeons tested HASP on 4 cases they had previously operated on: 3 with composite mandibular defects and 1 with a composite cervical spine defect. With the HASP stereographics and haptic feedback, using patient-specific computed tomography angiogram data, the surgeons planned the 4 cases, including bone resection, fibula design, recipient vessels selection, pedicle and perforator location selection, and skin paddle configuration.

Results: Some problems encountered during the actual surgery could have been avoided as they became evident with HASP. In one case, the fibula reconstruction was incomplete because the fibula had to be reversed and thus did not reach the temporal fossa. In another case, the fibula had to be rotated 180 degrees to correct the plate and screw placement in relation to the perforator. In the spinal case, difficulty in finding the optimal fibula shape and position required extra ischemia time.

Conclusions: The surgeons found HASP to be an efficient planning tool for FOFF reconstructions. The testing of alternative reconstructions to arrive at an optimal FOFF solution preoperatively potentially improves patient function and aesthetics and reduces operating room time.

Place, publisher, year, edition, pages
Wolters Kluwer, 2015
National Category
Medical Image Processing Surgery
Research subject
Computerized Image Processing
Identifiers
urn:nbn:se:uu:diva-260771 (URN)10.1097/GOX.0000000000000447 (DOI)
Available from: 2015-08-24 Created: 2015-08-24 Last updated: 2016-01-20Bibliographically approved
Olsson, P., Nysjö, F., Singh, N., Thor, A. & Carlbom, I. (2015). Visuohaptic bone saw simulator: Combining vibrotactile and kinesthetic feedback. In: Proc. 8th ACM SIGGRAPH Asia Technical Briefs: . Paper presented at ACM SIGGRAPH Asia 2015, November 2–5, Kobe, Japan (pp. 10:1-4). New York: ACM Press
Open this publication in new window or tab >>Visuohaptic bone saw simulator: Combining vibrotactile and kinesthetic feedback
Show others...
2015 (English)In: Proc. 8th ACM SIGGRAPH Asia Technical Briefs, New York: ACM Press, 2015, p. 10:1-4Conference paper, Published paper (Refereed)
Place, publisher, year, edition, pages
New York: ACM Press, 2015
National Category
Computer Vision and Robotics (Autonomous Systems)
Research subject
Computerized Image Processing
Identifiers
urn:nbn:se:uu:diva-262369 (URN)10.1145/2820903.2820925 (DOI)978-1-4503-3930-8 (ISBN)
Conference
ACM SIGGRAPH Asia 2015, November 2–5, Kobe, Japan
Available from: 2015-11-02 Created: 2015-09-14 Last updated: 2018-01-11Bibliographically approved
Organisations

Search in DiVA

Show all publications