**Fredrik Nysjö - Bioinformatician, SciLifeLab and Uppsala University** # Research # Publications [Google Scholar profile](https://scholar.google.se/citations?user=SI0wHoEAAAAJ&hl=en) ## PhD thesis ![ ](http://www.diva-portal.org/smash/get/diva2:1388179/PREVIEW01.jpg width="20%" border="1") Nysjö, F., "Modeling and Visualization for Virtual Interaction with Medical Image Data", PhD thesis, Uppsala University (2020) [(PDF)](http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-403104) Defended on March 13, 2020, with Prof. Alexandru C. Telea (Utrecht University) as opponent. Supervisors: Ingela Nyström, Filip Malmberg, and Ingrid Carlbom (Uppsala University). ## Pre-prints - Banerjee, S., Nysjö, F., Toumpanakis, D., Dhara, A.K., Wikström, J., and Strand, R., "AI-based Solution for Improving Neuroradiology Workflow for Cerebrovascular Structure Monitoring", submitted to journal (pre-print available at Research Square), (2022) [(PDF)](https://doi.org/10.21203/rs.3.rs-2372267/v1) ## Journal papers (peer-reviewed) - Pielawski, N., et al., "TissUUmaps 3: Improvements in Interactive Visualization, Exploration and Quality Assessment of Large-Scale Spatial Omics Data", Heliyon (Cell Press), (2023) [(PDF)](https://doi.org/10.1016/j.heliyon.2023.e15306) - Moafi, R., Nysjö, F., Kämpe, J., Riben, C., and Thor, A., "Haptic-Assisted Surgical Planning (HASP) In a Case of Bilateral Mandible Fracture", International Medical Case Report Journal, 2022:15 (2022) [(PDF)](https://doi.org/10.2147/IMCRJ.S380604) - Nilsson, J., Nysjö, F., Nyström, I., Kämpe, J., and Thor, A., "Evaluation of In-House, Haptic Assisted Surgical Planning for Virtual Reduction of Complex Mandibular Fractures," published online in International Journal of Computer Assisted Radiology and Surgery (IJCARS) (2021) [(PDF)](https://link.springer.com/content/pdf/10.1007/s11548-021-02353-w.pdf) - Nysjö, F., "Clustered Grid Cell Data Structure for Isosurface Rendering", Journal of WSCG, Vol.28, No.1-2, (2020). Also presented at WSCG 2020 (virtual conference), Pilsen, Czech Republic (2020). [(PDF)](http://wscg.zcu.cz/wscg2020/journal/E07.pdf) [(source code)](https://bitbucket.org/FredrikNysjo/grid_cells) - Nysjö, F., Malmberg, F., and Nyström, I., "RayCaching: Amortised Isosurface Rendering for Virtual Reality", Computer Graphics Forum (published online 2019), (2019). Also presented at Eurographics & Eurovis (EGEV) 2020 (virtual conference), Norrköping, Sweden (2020). [(PDF)](https://onlinelibrary.wiley.com/doi/pdf/10.1111/cgf.13762) [(source code)](https://bitbucket.org/FredrikNysjo/raycaching) - Nysjö, F., Olsson, P., Malmberg, F., Carlbom, I.B., and Nyström, I., "Using Anti-Aliased Signed Distance Fields for Generating Surgical Guides and Plates from CT Images", Journal of WSCG, Vol.25, No.1-2, (2017). Also presented at WSCG 2017, Pilsen, Czech Republic (2017). [(PDF)](http://wscg.zcu.cz/WSCG2017/!_2017_Journal_WSCG-No-1.pdf) - Olsson, P., Nysjö, F., Carlbom, I.B., and Johansson, S., "Comparison of Walking and Traveling-Wave Piezoelectric Motors as Actuators in Kinesthetic Haptic Devices," IEEE Transactions on Haptics, 9, (2016) [(PDF)](https://doi.org/10.1109/TOH.2016.2537803) - Svensson, L., Svensson, S., Nyström, I., Nysjö, F., Nysjö, J. et al., "ProViz: a tool for explorative 3-D visualization and template matching in electron tomograms", Journal of Computer Methods in Biomechanics and Biomedical Engineering: Imaging and Visualization 0 (2016) [(PDF)](https://doi.org/10.1080/21681163.2016.1154483) - Olsson, P., Nysjö, F., Rodriguez-Lorenzo, A., Thor, A., Hirsch, J.M., and Carlbom, I.B., "Novel Virtual Planning of Bone, Soft-tissue, and Vessels in Fibula Osteocutaneous Free Flaps with the Haptics-Assisted Surgery Planning (HASP) System", Plastic and Reconstructive Surgery Global Open (PRSGO) (2015) [(PDF)](http://dx.doi.org/10.1097/GOX.0000000000000447) - Olsson, P., Nysjö, F., Hirsch, J.M., and Carlbom, I.B., "A Haptics-Assisted Cranio-Maxillofacial Surgery Planning System for Restoring Skeletal Anatomy in Complex Trauma Cases," International Journal of Computer Assisted Radiology and Surgery (IJCARS) (2013) [(PDF)](http://dx.doi.org/10.1007/s11548-013-0827-5) ## Conference papers (peer-reviewed) - Blache, L., Nysjö, F., Malmberg, F., and Nyström, I., "SoftCut: A Virtual Planning Tool for Soft Tissue Resection on CT Images", MIUA 2018, Southampton, UK (2018) - Olsson, P., Nysjö, F., Singh, N., Thor, A., and Carlbom, I.B., "Visuohaptic Bone Saw Simulator: Combining Vibrotactile and Kinesthetic Feedback", ACM SIGGRAPH Asia 2015, Kobe, Japan (2015) [(PDF)](http://dx.doi.org/10.1145/2820903.2820925) - Nysjö, F., Olsson, P., Hirsch, J.M., and Carlbom, I.B., "Custom Mandibular Implant Design with Deformable Models and Haptics", Proc. Computer Assisted Radiology and Surgery (CARS) (abstract), Fukuoka, Japan (2014) [(PDF)](http://dx.doi.org/10.1007/s11548-014-1043-7) - Olsson, P., Nysjö, F., Aneer, B., Seipel, S., and Carlbom, I.B., "SplineGrip - An Eight Degrees-of-Freedom Flexible Haptic Sculpting Tool," ACM SIGGRAPH 2013 (abstract), Anaheim, USA (2013) [(PDF)](http://dx.doi.org/10.1145/2503385.2503440) - Olsson, P., Nysjö, F., Hirsch, J.M., and Carlbom, I.B., "A Haptics-Assisted Cranio-Maxillofacial Surgery Planning System for Restoring Skeletal Anatomy in Complex Trauma Cases," Proc. Computer Assisted Radiology and Surgery (CARS), Heidelberg, Germany (2013) - Olsson, P., Nysjö, F., Hirsch, J.M., and Carlbom, I.B., "Snap-to-Fit, a Haptic 6 DOF Alignment Tool for Virtual Assembly," IEEE World Haptics Conference, Daejeon, South Korea (2013) [(PDF)](http://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=6548409) - Olsson, P., Johansson, S., Nysjö, F., and Carlbom, I.B., "Rendering Stiffness with a Prototype Haptic Glove Actuated by an Integrated Piezoelectric Motor," Euro Haptics Conference, Tampere, Finland (2012) [(PDF)](http://dx.doi.org/10.1007/978-3-642-31401-8_33) - Olsson, P., Nysjö, F., Seipel, S., and Carlbom, I.B., "Physically Co-Located Haptic Interaction with 3D Displays," Haptics Symposium, Vancouver, Canada (2012) [(PDF)](http://dx.doi.org/10.1109/HAPTIC.2012.6183801) ## Conference papers (non peer-reviewed) - Nysjö, F., Malmberg, F., Nyström, I., "RayCaching: Point-Based Isosurface Rendering for Large Volume Datasets," presented at SSBA Symposium 2018, Stockholm (2018) - Nysjö, F., Olsson, P., Malmberg, F., Carlbom, I.B., Nyström, I., "Signed Distance Fields for Modeling Surgical Guides and Plates," presented at SSBA Symposium 2016, Uppsala (2016) ## Book chapters - Nyström, I., Olsson, P., Nysjö, J., Nysjö, F., Malmberg, F. et al., "Virtual Cranio-Maxillofacial Surgery Planning with Stereo Graphics and Haptics," in Ritacco, Lucas E., Milano, Federico E., Chao, Edmund (red.) Computer-Assisted Musculoskeletal Surgery, Springer International Publishing. 29-42, (2016) ## Other publications - Nysjö, F., "Rendering Software for Multiple Projectors," MSc thesis, Department of Information Technology, Uppsala University (2011) [(PDF)](http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-161644) # Teaching ## Courses (mostly undergraduate level) - Computer Graphics (1TD388/1MD150):
Spring 2016-2022 [(Course description and syllabus)](https://www.uu.se/en/admissions/freestanding-courses/course-syllabus/?kpid=38401&lasar=22%2F23&typ=1) [(GitHub page)](https://github.com/cg-uu) - Scientific Visualization (1TD389/1MD140):
Fall 2016-2021 [(Course description and syllabus)](https://www.uu.se/en/admissions/freestanding-courses/course-syllabus/?kpid=38796&lasar=22%2F23&typ=1) [(GitHub page)](https://github.com/vetvis-uu) - Scientific Visualization (graduate course):
Fall 2015, 2016, 2018, 2020 [(Course webpage from 2018)](https://andershast.com/home/course/scientific-visualisation-graduate-course/) - Medical Informatics (1MD030):
Fall 2020 [(Course description and syllabus)](https://www.uu.se/en/admissions/freestanding-courses/course-syllabus/?kpid=42031&lasar=22%2F23&typ=1) - Imperative and Object-Oriented Programming (1DL221):
Fall 2020 - Advanced Interaction Design (1MD001):
Spring 2016 ## Master thesis supervision - Thesis projects where I have been [supervisor](http://uu.diva-portal.org/smash/resultList.jsf?query=&language=en&searchType=UNDERGRADUATE&noOfRows=50&sortOrder=author_sort_asc&sortOrder2=title_sort_asc&onlyFullText=false&sf=all&aq=%5B%5B%7B%22supervisor%22%3A%5B%22Nysj%C3%B6%2C+Fredrik%22%5D%7D%5D%5D&aqe=%5B%5D&aq2=%5B%5B%5D%5D&af=%5B%5D) or [reviewer](http://uu.diva-portal.org/smash/resultList.jsf?query=&language=en&searchType=UNDERGRADUATE&noOfRows=50&sortOrder=author_sort_asc&sortOrder2=title_sort_asc&onlyFullText=false&sf=all&aq=%5B%5B%7B%22examiner%22%3A%5B%22Nysj%C3%B6%2C+Fredrik%22%5D%7D%5D%5D&aqe=%5B%5D&aq2=%5B%5B%5D%5D&af=%5B%5D). # Other activities - My [Bitbucket](https://bitbucket.org/FredrikNysjo/workspace/repositories) and [GitHub](https://github.com/FredrikNysjo) pages. - My computer graphics and graphics programming related work (including some personal projects): https://fredriknysjo.bitbucket.io # CV My full CV can be found [here](https://fredriknysjo.bitbucket.io/cv.html). # Contact
Fredrik Nysjö
Department of Information Technology,
Division of Vi3, Image Analysis
Box 337
751 05 Uppsala		 Office room: 104136 (Ångström, House 10)
E-mail: fredrik.nysjo@it.uu.se