Filip Malmberg
Senior Lecturer/Associate Professor at Department of Information Technology; Vi3; Image Analysis
- Telephone:
- +46 18 471 53 08
- E-mail:
- filip.malmberg@it.uu.se
- Visiting address:
- Hus 10, Regementsvägen 10
- Postal address:
- Box 337
751 05 UPPSALA
Short presentation
Filip Malmberg is a researcher in computerized image analysis, working at the Department of Information Technology.

Publications
Recent publications
Points2Regions: Fast, interactive clustering of imaging-based spatial transcriptomics data
Part of Cytometry Part A, 2024
- DOI for Points2Regions: Fast, interactive clustering of imaging-based spatial transcriptomics data
- Download full text (pdf) of Points2Regions: Fast, interactive clustering of imaging-based spatial transcriptomics data
A whole-body diffusion MRI normal atlas: development, evaluation and initial use
Part of Cancer Imaging, 2023
- DOI for A whole-body diffusion MRI normal atlas: development, evaluation and initial use
- Download full text (pdf) of A whole-body diffusion MRI normal atlas: development, evaluation and initial use
A Practical Algorithm for Max-Norm OptimalBinary Labeling of Graphs
Part of Graph-Based Representations in Pattern Recognition, 2023
Cell Segmentation of in situ Transcriptomics Data using Signed Graph Partitioning
Part of Graph-Based Representations in Pattern Recognition, p. 139-148, 2023
Part of Journal of Hepatology, 2022
All publications
Articles in journal
Points2Regions: Fast, interactive clustering of imaging-based spatial transcriptomics data
Part of Cytometry Part A, 2024
- DOI for Points2Regions: Fast, interactive clustering of imaging-based spatial transcriptomics data
- Download full text (pdf) of Points2Regions: Fast, interactive clustering of imaging-based spatial transcriptomics data
A whole-body diffusion MRI normal atlas: development, evaluation and initial use
Part of Cancer Imaging, 2023
- DOI for A whole-body diffusion MRI normal atlas: development, evaluation and initial use
- Download full text (pdf) of A whole-body diffusion MRI normal atlas: development, evaluation and initial use
Part of Journal of Hepatology, 2022
Guest Editorial: Discrete Geometry and Mathematical Morphology
Part of Journal of Mathematical Imaging and Vision, p. 691-692, 2022
Part of Fluids and Barriers of the CNS, 2022
- DOI for White matter changes should not exclude patients with idiopathic normal pressure hydrocephalus from shunt surgery
- Download full text (pdf) of White matter changes should not exclude patients with idiopathic normal pressure hydrocephalus from shunt surgery
Part of Scientific Reports, 2022
- DOI for Improved geometric accuracy of whole body diffusion-weighted imaging at 1.5T and 3T using reverse polarity gradients
- Download full text (pdf) of Improved geometric accuracy of whole body diffusion-weighted imaging at 1.5T and 3T using reverse polarity gradients
Faster dense deformable image registration by utilizing both CPU and GPU
Part of Journal of Medical Imaging, 2021
- DOI for Faster dense deformable image registration by utilizing both CPU and GPU
- Download full text (pdf) of Faster dense deformable image registration by utilizing both CPU and GPU
Fast graph-cut based optimization for practical dense deformable registration of volume images
Part of Computerized Medical Imaging and Graphics, 2020
Multiple comparison correction methods for whole-body magnetic resonance imaging
Part of Journal of Medical Imaging, 2020
- DOI for Multiple comparison correction methods for whole-body magnetic resonance imaging
- Download full text (pdf) of Multiple comparison correction methods for whole-body magnetic resonance imaging
Part of Scientific Reports, 2020
- DOI for Validation of automated whole-body analysis of metabolic and morphological parameters from an integrated FDG-PET/MRI acquisition
- Download full text (pdf) of Validation of automated whole-body analysis of metabolic and morphological parameters from an integrated FDG-PET/MRI acquisition
Two Polynomial Time Graph Labeling Algorithms Optimizing Max-Norm-Based Objective Functions
Part of Journal of Mathematical Imaging and Vision, p. 737-750, 2020
RayCaching: Amortized Isosurface Rendering for Virtual Reality
Part of Computer graphics forum (Print), p. 220-230, 2020
- DOI for RayCaching: Amortized Isosurface Rendering for Virtual Reality
- Download full text (pdf) of RayCaching: Amortized Isosurface Rendering for Virtual Reality
Part of Acta Ophthalmologica, p. 208-213, 2019
A whole-body FDG PET/MR atlas for multiparametric voxel-based analysis
Part of Scientific Reports, 2019
- DOI for A whole-body FDG PET/MR atlas for multiparametric voxel-based analysis
- Download full text (pdf) of A whole-body FDG PET/MR atlas for multiparametric voxel-based analysis
Average volume reference space for large scale registration of whole-body magnetic resonance images
Part of PLOS ONE, 2019
- DOI for Average volume reference space for large scale registration of whole-body magnetic resonance images
- Download full text (pdf) of Average volume reference space for large scale registration of whole-body magnetic resonance images
PDNet: Semantic segmentation integrated with a primal-dual network for document binarization
Part of Pattern Recognition Letters, p. 52-60, 2019
- DOI for PDNet: Semantic segmentation integrated with a primal-dual network for document binarization
- Download full text (pdf) of PDNet: Semantic segmentation integrated with a primal-dual network for document binarization
Part of European Journal of Nuclear Medicine and Molecular Imaging, 2018
Using anti-aliased signed distance fields for generating surgical guides and plates from CT images
Part of Journal of WSCG, p. 11-20, 2017
Exact Evaluation of Targeted Stochastic Watershed Cuts
Part of Discrete Applied Mathematics, p. 449-460, 2017
A concept for holistic whole body MRI data analysis, Imiomics
Part of PLOS ONE, 2017
- DOI for A concept for holistic whole body MRI data analysis, Imiomics
- Download full text (pdf) of A concept for holistic whole body MRI data analysis, Imiomics
SmartPaint: a tool for interactive segmentation of medical volume images
Part of Computer Methods In Biomechanics And Biomedical Engeineering-Imaging And Visualization, p. 36-44, 2017
Part of Annals of Oncology, 2017
Part of Skeletal Radiology, p. 763-769, 2016
Part of Investigative Ophthalmology and Visual Science, 2016
BoneSplit - A 3D Texture Painting Tool for Interactive Bone Separation in CT Images
Part of Journal of WSCG, p. 157-166, 2015
Part of Psychiatry Research, p. 227-235, 2015
Efficient algorithm for finding the exact minimum barrier distance
Part of Computer Vision and Image Understanding, p. 53-64, 2014
Evaluation of prostate segmentation algorithms for MRI: The PROMISE12 challenge
Part of Medical Image Analysis, p. 359-373, 2014
Canine body composition quantification using 3 tesla fat–water MRI
Part of Journal of Magnetic Resonance Imaging, p. 485-491, 2014
An efficient algorithm for exact evaluation of stochastic watersheds
Part of Pattern Recognition Letters, p. 80-84, 2014
Part of Obesity, 2013
Part of NeuroImage, p. 355-360, 2013
Shape and volume of craniofacial cavities in intentional skull deformations
Part of American Journal of Physical Anthropology, p. 110-119, 2013
Part of Computer Vision and Image Understanding, p. 429-437, 2013
Bisphenol A exposure increases liver fat in juvenile fructose-fed Fischer 344 rats
Part of Toxicology, p. 125-132, 2013
A Graph-based Framework for Sub-pixel Image Segmentation
Part of Theoretical Computer Science, p. 1338-1349, 2011
Part of Nuclear Instruments and Methods in Physics Research Section A, p. 143-148, 2011
Läkarens känsel hjälper datorn
Part of Forskning & Framsteg, p. 62, 2009
Part of International Journal of Adhesion and Adhesives, p. 551-557, 2009
Books
Collections (editor)
Springer, 2021
Comprehensive doctoral thesis
Comprehensive licentiate thesis
Conference papers
A Practical Algorithm for Max-Norm OptimalBinary Labeling of Graphs
Part of Graph-Based Representations in Pattern Recognition, 2023
Cell Segmentation of in situ Transcriptomics Data using Signed Graph Partitioning
Part of Graph-Based Representations in Pattern Recognition, p. 139-148, 2023
Optimization of max-norm objective functions in image processing and computer vision
Part of Discrete Geometry for Computer Imagery, p. 206-218, 2019
SoftCut: A Virtual Planning Tool for Soft Tissue Resection on CT Images
Part of Medical Image Understanding and Analysis, p. 299-310, 2018
When Can lp-norm Objective Functions Be Minimized via Graph Cuts?
Part of Combinatorial Image Analysis, p. 112-117, 2018
Part of Ophthalmic Technologies XXVII, 2017
BoneSplit – A 3D painting tool for interactive bone segmentation in CT images
Part of Pattern Recognition and Information Processing, p. 3-13, 2017
The Boolean Map Distance: Theory and Efficient Computation
Part of International Conference on Discrete Geometry for Computer Imagery, p. 335-346, 2017
The Minimum Barrier Distance: A Summary of Recent Advances
Part of Discrete Geometry for Computer Imagery. DGCI 2017, p. 57-68, 2017
- DOI for The Minimum Barrier Distance: A Summary of Recent Advances
- Download full text (pdf) of The Minimum Barrier Distance: A Summary of Recent Advances
Holistic whole-body MRI image analysis
Part of Symposium of the Swedish Society for Automated Image Analysis, Uppsala, Sweden, (SSBA), 2016
Part of Ophthalmic Technologies XXVI, 2016
A Toolbox for Non-parametric Deformable Registration of Volume Images
2016
Part of Ophthalmic Technologies XXVI, 2016
Signed Distance Fields for Modeling Surgical Guides and Plates from CT Images
Part of Proc, Swedish Symposium on Image Analysis, 2016
Interactive Deformation of Volume Images for Image Registration
Part of Proc. Interactive Medical Image Computing Workshop, 2015
Fast evaluation of the robust stochastic watershed
Part of Mathematical Morphology and Its Applications to Signal and Image Processing, p. 705-716, 2015
An interactive tool for deformable registration of volume images
Part of Symposium of the Swedish Society for Automated Image Analysis (SSBA), 2014
Exact evaluation of stochastic watersheds: From trees to general graphs
Part of Discrete Geometry for Computer Imagery, p. 309-319, 2014
The Minimum Barrier Distance - Stability to seed point position
Part of Discrete Geometry for Computer Imagery, DGCI 2014, p. 111-121, 2014
Precise 3D Angle Measurements in CT Wrist Images
Part of Image Analysis and Processing – ICIAP 2013, p. 479-488, 2013
Faster Fuzzy Connectedness via Precomputation
Part of Mathematical Morphology and Its Applications to Signal and Image Processing, p. 476-483, 2013
Towards User-Guided Quantitative Evaluation of Wrist Fractures in CT Images
Part of Computer Vision and Graphics, p. 204-211, 2012
Seeded Segmentation Based on Object Homogeneity
Part of Proceedings of the 21st International Conference on Pattern Recognition (ICPR), p. 21-24, 2012
Smart Paint: A New Interactive Segmentation Method\\ Applied to MR Prostate Segmentation
Part of Prostate MR Image Segmentation Grand Challenge (PROMISE'12), a MICCAI 2012 workshop, 2012
Part of Visual Informatics: Sustaining Research and Innovations, p. 1-12, 2011
Generalized Hard Constraints for Graph Segmentation
Part of Image Analysis, 17th Scandinavian Conference. SCIA 2011., 2011
Image Foresting Transform: On-the-fly Computation of Segmentation Boundaries
Part of Image Analysis: 17th Scandinavian Conference, SCIA 2011, 2011
Relaxed Image Foresting Transforms for Interactive Volume Image Segmentation
Part of MEDICAL IMAGING 2010, 2010
Segmentation and Visualization of 3D Medical Images through Haptic Rendering
Part of Proceedings of the 10th International Conference on Pattern Recognition and Information Processing (PRIP 2009), p. 43-48, 2009
Interactive Segmentation with Relaxed Image Foresting Transforms
Part of Proceedings of SSBA 2009, 2009
Sub-pixel Segmentation with the Image Foresting Transform
Part of Proceedings of International Workshop on Combinatorial Image Analysis, p. 201-211, 2009
Binarization of Phase Contrast Volume Images of Fibrous Materials: A Case Study
Part of Proceedings of International Conference on Computer Vision Theory and Applications (VISAPP 2009), p. 148-153, 2009
An Automated Image Analysis Method for Measuring Fibre Contact in Fibrous and Composite Materials
Part of 13th European Conference on Composite Materials (ECCM), 2008
Graph Cut Based Segmentation of Phase Contrast Volume Images of Fibrous Materials
Part of Proceedings of Swedish Symposium on Image Analysis (SSBA'08), p. 131-134, 2008
Minimal Cost-Path for Path-Based Distances
Part of Proceedings of 5th International Symposium on Image and Signal Processing and Analysis (ISPA 2007), p. 379-384, 2007
Part of Progress in Paper Physics Seminar, Oxford, Ohio, 2006, 2006
Part of 2006 Progress in Paper Physics, 2006
Part of 2006 Progress in Paper Physics, 2006
A 3D live-wire segmentation method for volume images using haptic interaction
Part of DISCRETE GEOMETRY FOR COMPUTER IMAGERY, PROCEEDINGS 4245, p. 663-673, 2006
Manuscripts (preprints)
CalligraphyNet: Augmenting handwriting generation with quill based stroke width
2019
A toolkit for interactive medical image visualization and segmentation with haptics
2008
Faster dense deformable image registration by utilizing both CPU and GPU
Vectorised High-Fidelity Haptic Rendering with Dynamic Pointshell
Deformable Image Registration of Volumetric Whole-body MRI: An Evaluation
Rapid and Precise Orbit Segmentation through Interactive 3D Painting