Natasa Sladoje
Professor at Department of Information Technology; Vi3; Image Analysis
- Telephone:
- +46 18 471 49 12
- E-mail:
- natasa.sladoje@it.uu.se
- Visiting address:
- Hus 10, Regementsvägen 10
- Postal address:
- Box 524
751 20 UPPSALA
- Academic merits:
- Docent
- ORCID:
- 0000-0002-6041-6310
Short presentation
I am Professor in Computerized Image Analysis at the Dept. of Information Technology, Uppsala University. I am interested in development of image analysis methods, applications of machine and deep learning in image analysis, and applications of our developed tools in all fields of science and everyday life where image data is relevant and its automated analysis is required. For more details, read about MIDA-group which I am leading.
Keywords
- artificial intelligence
- image analysis
- deep learning
- biomedical image analysis
- data-driven life science
- information and communication technology (ict)
- image processing
- medical image analysis
- algorithm development
- discrete geometry
- pattern recognition
Research

Publications
Recent publications
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Roadmap on deep learning for microscopy
Part of JPhys Photonics, 2026
- DOI for Roadmap on deep learning for microscopy
- Download full text (pdf) of Roadmap on deep learning for microscopy
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Part of Lung Cancer, 2026
- DOI for Incremental prognostic value of immune cell densities beyond clinical parameters in non-small cell lung cancer
- Download full text (pdf) of Incremental prognostic value of immune cell densities beyond clinical parameters in non-small cell lung cancer
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Isolated Channel Vision Transformers: From Single-Channel Pretraining to Multi-Channel Finetuning
Part of 36th British Machine Vision Conference 2025, {BMVC} 2025, p. 1-14, 2025
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Learn2Reg 2024: New Benchmark Datasets Driving Progress on New Challenges
Part of Machine Learning for Biomedical Imaging, p. 775-791, 2025
- DOI for Learn2Reg 2024: New Benchmark Datasets Driving Progress on New Challenges
- Download full text (pdf) of Learn2Reg 2024: New Benchmark Datasets Driving Progress on New Challenges
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Towards robust bubble detection in diverse microphysiological systems by machine learning
2025
All publications
Articles in journal
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Roadmap on deep learning for microscopy
Part of JPhys Photonics, 2026
- DOI for Roadmap on deep learning for microscopy
- Download full text (pdf) of Roadmap on deep learning for microscopy
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Part of Lung Cancer, 2026
- DOI for Incremental prognostic value of immune cell densities beyond clinical parameters in non-small cell lung cancer
- Download full text (pdf) of Incremental prognostic value of immune cell densities beyond clinical parameters in non-small cell lung cancer
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Learn2Reg 2024: New Benchmark Datasets Driving Progress on New Challenges
Part of Machine Learning for Biomedical Imaging, p. 775-791, 2025
- DOI for Learn2Reg 2024: New Benchmark Datasets Driving Progress on New Challenges
- Download full text (pdf) of Learn2Reg 2024: New Benchmark Datasets Driving Progress on New Challenges
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Part of Computers in Biology and Medicine, p. 1-14, 2025
- DOI for Let it shine: Autofluorescence of Papanicolaou-stain improves AI-based cytological oral cancer detection
- Download full text (pdf) of Let it shine: Autofluorescence of Papanicolaou-stain improves AI-based cytological oral cancer detection
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UpStory: the uppsala storytelling dataset
Part of Frontiers in Robotics and AI, 2025
- DOI for UpStory: the uppsala storytelling dataset
- Download full text (pdf) of UpStory: the uppsala storytelling dataset
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Part of PLOS ONE, 2024
- DOI for Deep multiple instance learning versus conventional deep single instance learning for interpretable oral cancer detection
- Download full text (pdf) of Deep multiple instance learning versus conventional deep single instance learning for interpretable oral cancer detection
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Cross-modality sub-image retrieval using contrastive multimodal image representations
Part of Scientific Reports, 2024
- DOI for Cross-modality sub-image retrieval using contrastive multimodal image representations
- Download full text (pdf) of Cross-modality sub-image retrieval using contrastive multimodal image representations
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Part of Scientific Reports, 2023
- DOI for Automated detection, segmentation and measurement of major vessels and the trachea in CT pulmonary angiography
- Download full text (pdf) of Automated detection, segmentation and measurement of major vessels and the trachea in CT pulmonary angiography
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INSPIRE: Intensity and Spatial Information-Based Deformable Image Registration
Part of PLOS ONE, 2023
- DOI for INSPIRE: Intensity and Spatial Information-Based Deformable Image Registration
- Download full text (pdf) of INSPIRE: Intensity and Spatial Information-Based Deformable Image Registration
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Is image-to-image translation the panacea for multimodal image registration?: A comparative study
Part of PLOS ONE, 2022
- DOI for Is image-to-image translation the panacea for multimodal image registration?: A comparative study
- Download full text (pdf) of Is image-to-image translation the panacea for multimodal image registration?: A comparative study
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Part of Pattern Recognition Letters, p. 196-203, 2022
- DOI for Fast computation of mutual information in the frequency domain with applications to global multimodal image alignment
- Download full text (pdf) of Fast computation of mutual information in the frequency domain with applications to global multimodal image alignment
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Part of Scientific Data, 2020
- DOI for HISTOBREAST: a collection of brightfield microscopy images of Haematoxylin and Eosin stained breast tissue
- Download full text (pdf) of HISTOBREAST: a collection of brightfield microscopy images of Haematoxylin and Eosin stained breast tissue
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Part of Patterns (New York, N.Y.), 2020
- DOI for BIAFLOWS: A Collaborative Framework to Reproducibly Deploy and Benchmark Bioimage Analysis Workflows.
- Download full text (pdf) of BIAFLOWS: A Collaborative Framework to Reproducibly Deploy and Benchmark Bioimage Analysis Workflows.
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Stochastic Distance Transform: Theory, Algorithms and Applications
Part of Journal of Mathematical Imaging and Vision, p. 751-769, 2020
- DOI for Stochastic Distance Transform: Theory, Algorithms and Applications
- Download full text (pdf) of Stochastic Distance Transform: Theory, Algorithms and Applications
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Generalised deep learning framework for HEp-2 cell recognition using local binary pattern maps
Part of IET Image Processing, p. 1201-1208, 2020
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Part of Journal of Electronic Imaging (JEI), 2019
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Part of IEEE Transactions on Image Processing, p. 3584-3597, 2019
- DOI for Fast and Robust Symmetric Image Registration Based on Distances Combining Intensity and Spatial Information
- Download full text (pdf) of Fast and Robust Symmetric Image Registration Based on Distances Combining Intensity and Spatial Information
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Facilitating Ultrastructural Pathology through Automated Imaging and Analysis
Part of Journal of Pathology Informatics, p. 38-39, 2019
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Part of IEEE Access, p. 53080-53091, 2018
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Part of Journal of Electronic Imaging (JEI), 2016
- DOI for Restoration of images degraded by signal-dependent noise based on energy minimization: an empirical study
- Download full text (pdf) of Restoration of images degraded by signal-dependent noise based on energy minimization: an empirical study
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Estimation of Feret's diameter from pixel coverage representation of a shape
Part of Pattern Recognition Letters, p. 37-45, 2016
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Estimation of linear deformations of 2D and 3D fuzzy objects
Part of Pattern Recognition, p. 1391-1403, 2015
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Precise Euclidean distance transforms in 3D from voxel coverage representation
Part of Pattern Recognition Letters, p. 184-191, 2015
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Linear time distances between fuzzy sets with applications to pattern matching and classification
Part of IEEE Transactions on Image Processing, p. 126-136, 2014
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A new set distance and its application to shape registration
Part of Pattern Analysis and Applications, p. 141-152, 2014
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Coverage segmentation based on linear unmixing and minimization of perimeter and boundary thickness
Part of Pattern Recognition Letters, p. 728-738, 2012
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A Graph-based Framework for Sub-pixel Image Segmentation
Part of Theoretical Computer Science, p. 1338-1349, 2011
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Regularized image denoising based on spectral gradient optimization
Part of Inverse Problems, 2011
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Defuzzification of spatial fuzzy sets by feature distance minimization
Part of Image and Vision Computing, p. 127-141, 2011
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High-precision boundary length estimation by utilizing gray-level information
Part of IEEE Transactions on Pattern Analysis and Machine Intelligence, p. 357-363, 2009
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Representation and Reconstruction of Fuzzy Disks by Moments
Part of Fuzzy sets and systems (Print), p. 517-534, 2007
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Measurements of digitized objects with fuzzy borders in 2D and 3D
Part of Image and Vision Computing, p. 123-132, 2005
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Shape signaturs of fuzzy star-shaped sets based on distance from the centroid
Part of Pattern Recognition Letters, p. 735-746, 2005
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Efficiency of Characterizing Ellipses and Ellipsoids by Discrete Moments
Part of IEEE Transactions on Pattern Analysis and Machine Intelligence, p. 407-414, 2000
Articles, review/survey
Chapters in book
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Introduction: computer-assisted analysis of multimodal image data
Part of Imaging Modalities for Biological and Preclinical Research, Institute of Physics Publishing (IOPP), 2021
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Computer-assisted analysis of multimodal image data—perspectives and conclusion
Part of Imaging Modalities for Biological and Preclinical Research, Institute of Physics Publishing (IOPP), 2021
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The coverage model and its use in image processing
Part of Selected Topics on Image Processing and Cryptology, p. 39-117, Mathematical Institute of the Serbian Academy of Sciences and Arts, 2012
Collections (editor)
Conference papers
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Isolated Channel Vision Transformers: From Single-Channel Pretraining to Multi-Channel Finetuning
Part of 36th British Machine Vision Conference 2025, {BMVC} 2025, p. 1-14, 2025
-
Towards robust bubble detection in diverse microphysiological systems by machine learning
2025
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A Comparison of Deep Learning Methods for Cell Detection in Digital Cytology
Part of Image Analysis, p. 264-277, 2025
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Part of Pattern Recognition, p. 408-421, 2024
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Part of Detection of Extremely Sparse Key Instances in Whole Slide Cytology Images via Self-supervised One-class Representation Learning, p. 408-421, 2024
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Are We Friends?: End-to-End Prediction of Child Rapport in Guided Play
Part of Computer Vision – ECCV 2024 Workshops, p. 380-392, 2024
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Part of Pattern Recognition and Image Analysis, p. 261-275, 2023
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2023
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Partial dimensional collapse in contrastive learning when using intermediate layers
2023
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Contrastive Learning of Equivariant Image Representations for Multimodal Deformable Registration
Part of 2023 IEEE 20th International Symposium on Biomedical Imaging (ISBI), 2023
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2023
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Rotationally Equivariant Representation Learning for Multimodal Images
2022
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2022
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DCNN based Oral Cancer Screening using Whole Slide Cytology Images: Effect of Increased Patch Size
2022
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Label-Free Reverse Image Search of Multimodal Microscopy Images
2022
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Re-Ranking Strategies in Cross-Modality Microscopy Retrieval
2022
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Efficient Algorithms for Global Multimodal Image Registration
2022
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Part of ICMI '22, p. 444-454, 2022
- DOI for End-to-End Learning and Analysis of Infant Engagement During Guided Play: Prediction and Explainability
- Download full text (pdf) of End-to-End Learning and Analysis of Infant Engagement During Guided Play: Prediction and Explainability
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End-to-end Multiple Instance Learning with Gradient Accumulation
Part of 2022 IEEE International Conference on Big Data (Big Data), p. 2742-2746, 2022
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Part of Companion Publication of the 2021 International Conference on Multimodal Interaction, p. 403-407, 2021
- DOI for Automatic Analysis of Infant Engagement during Play: An End-to-end Learning and Explainable AI Pilot Experiment
- Download full text (pdf) of Automatic Analysis of Infant Engagement during Play: An End-to-end Learning and Explainable AI Pilot Experiment
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The Effect of Within-Bag Sampling on End-to-End Multiple Instance Learning
Part of Proceedings of the 12th International Symposium on Image and Signal Processing and Analysis (ISPA), p. 183-188, 2021
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Contrastive Learning for Equivariant Multimodal Image Representations
2021
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Image-to-Image Translation in Multimodal Image Registration: How Well Does It Work?
2021
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2021
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Registration of Multimodal Microscopy Images using CoMIR – learned structural image representations
2021
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Comir: Contrastive multimodal image representation for registration
2021
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CoMIR: Contrastive Multimodal Image Representation for Registration
Part of NeurIPS - 34th Conference on Neural Information Processing Systems, 2020
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Part of 2020 IEEE 17th International Symposium on Biomedical Imaging (ISBI), p. 517-521, 2020
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Part of 4th NEUBIAS Conference, Bordeaux, France, 2020
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Part of 4th NEUBIAS Conference, Bordeaux, France, 2020
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A Deep Learning Based Pipeline for Efficient Oral Cancer Screening on Whole Slide Images
Part of Image Analysis and Recognition, p. 249-261, 2020
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Towards automated multiscale Glomeruli detection and analysis in TEM by fusion of CNN and LBP maps
Part of 3rd NEUBIAS Conference, 2019
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On the Effectiveness of Generative Adversarial Networks as HEp-2 Image Augmentation Tool
Part of Scandinavian Conference on Image Analysis, p. 439-451, 2019
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Part of 3rd NEUBIAS Conference, Luxembourg, 2-8 February 2019, 2019
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Part of Computer Vision, p. 465-475, 2019
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Oral Cancer Detection: A Comparison of Texture Focused Deep Learning Approaches
Part of Proceedings of the Swedish Society for Automated Image Analysis (SSBA), 2019
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Robust Symmetric Affine Image Registration
Part of Swedish Symposium on Image Analysis, 2019
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Stochastic Distance Functions with Applications in Object Detection and Image Segmentation
Part of Swedish Symposium on Image Analysis, 2019
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Part of Discrete Geometry for Computer Imagery, p. 75-86, 2019
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Texture-based oral cancer detection: A performance analysis of deep learning approaches.
Part of 3rd NEUBIAS Conference, 2019
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Part of Swedish Symposium on Deep Learning, 2018
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Denoising of Short Exposure Transmission Electron Microscopy Images using CNN
Part of Swedish Symposium on Image Analysis, 2018
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Denoising of short exposure transmission electron microscopy images for ultrastructural enhancement
Part of Proc. 15th International Symposium on Biomedical Imaging, p. 921-925, 2018
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Part of Swedish Symposium on Image Analysis, 2018
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Part of Image Analysis, p. 362-374, 2017
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Part of Swedish Symposium on Image Analysis, 2017
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Part of Swedish Symposium on Image Analysis, 2017
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Part of Mathematical Morphology and its Applications to Signal and Image Processing, p. 395-407, 2017
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Part of In Proc. of the 18th International Workshop on Combinatorial Image Analysis, IWCIA2017, p. 243-255, 2017
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Part of Image Analysis, p. 407-418, 2017
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Part of Proceedings of the Swedish Society for Automated Image Analysis, p. 137-141, 2016
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Signature of a Shape Based on Its Pixel Coverage Representation
Part of Discrete Geometry for Computer Imagery, DGCI 2016. Lecture Notes in Computer Science, Vol. 9647, pp. 181-193, Springer 2016, p. 181-193, 2016
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Part of 2016 Ieee 13Th International Symposium On Biomedical Imaging (ISBI), p. 123-127, 2016
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Part of Biomedical Imaging (ISBI), 2016 IEEE 13th International Symposium on, p. 386-390, 2016
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Single image super-resolution reconstruction in presence of mixed Poisson-Gaussian noise
Part of 2016 SIXTH INTERNATIONAL CONFERENCE ON IMAGE PROCESSING THEORY, TOOLS AND APPLICATIONS (IPTA), 2016
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Coverage segmentation of 3D thin structures
Part of Proc. 5th International Conference on Image Processing Theory, Tools and Applications, p. 23-28, 2015
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Microscopy image enhancement for cost-effective cervical cancer screening
Part of Image Analysis, p. 440-451, 2015
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High-resolution reconstruction by feature distance minimization from multiple views of an object
Part of Proc. 5th International Conference on Image Processing Theory, Tools and Applications, p. 29-34, 2015
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αLBP – a novel member of the Local Binary Pattern family based on α-cutting
Part of Proc. 9th International Symposium on Image and Signal Processing and Analysis, p. 13-18, 2015
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Exact linear time Euclidean distance transforms of grid line sampled shapes
Part of Mathematical Morphology and its Applications to Signal and Image Processing, p. 645-656, 2015
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Optimizing optics and imaging for pattern recognition based screening tasks
Part of Proc. 22nd International Conference on Pattern Recognition, p. 3333-3338, 2014
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An evaluation of potential functions for regularized image deblurring
Part of Image Analysis and Recognition, p. 150-158, 2014
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Coverage segmentation of thin structures by linear unmixing and local centre of gravity attraction
Part of Proc. 8th International Symposium on Image and Signal Processing and Analysis, p. 83-88, 2013
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Distance measures between digital fuzzy objects and their applicability in image processing
Part of Combinatorial Image Analysis, p. 385-397, 2011
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Precise Estimation of the Projection of a Shape from a Pixel Coverage Representation
Part of Proceedings of the 7th IEEE International Symposium on Image and Signal Processing and Analysis (ISPA), p. 569-574, 2011
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The Sum of minimal distances as a useful distance measure for image registration
Part of Proceedings SSBA 2010, p. 55-58, 2010
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De-noising of SRµCT Fiber Images by Total Variation Minimization
Part of Proceedings of the 20th International Conference on Pattern Recognition (ICPR10), p. 4621-4624, 2010
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Estimation of linear deformations of 3D objects
Part of Proceedings of 2010 IEEE 17th International Conference on Image Processing, p. 153-156, 2010
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On set distances and their application to image registration
Part of Proc. 6th International Symposium on Image and Signal Processing and Analysis, p. 449-454, 2009
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Improved Quantification of Bone Remodelling by Utilizing Fuzzy Based Segmentation
Part of Image Analysis, p. 750-759, 2009
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Recovering Affine Deformations of Fuzzy Shapes
Part of 16th Scandinavian Conference on Image Analysis, p. 735-744, 2009
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Pixel Coverage Segmentation for Improved Feature Estimation
Part of 15th International Conference on Image Analysis and Processing, p. 929-938, 2009
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Deterministic Defuzzification based on Spectral Projected Gradient Optimization
Part of 30th Symposium of the German Association for Pattern Recognition (DAGM), p. 476-485, 2008
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Defuzzification by Feature Distance Minimization Based on DC Programming
Part of 5th International Symposium on Image and Signal Processing and Analysis, 2007, p. 373-378, 2007
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Feature Based Defuzzification at Increased Spatial Resolution
Part of Combinatorial Image Analysis, p. 131-143, 2006
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Feature Based Defuzzification in Z² and Z³ Using a Scale Space Approach
Part of Discrete Geometry for Computer Imagery 13th International Conference, DGCI 2006, Szeged, Hungary, October 25-27, 2006. Proceedings, p. 379-390, 2006
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Estimation of moments of digitized objects with fuzzy borders
Part of Proc. of 13th International Conference on Image Analysis and Processing, p. 188-195, 2005
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Defuzzification of discrete objects by optimizing area and perimeter similarity
Part of Proceedings of International Conference on Pattern Recognition (ICPR 2004), p. 526-629, 2004
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Shape Description of Fuzzy Segmented Objects: Area and Perimeter Estimators
Part of Proceedings of SSAB (Swedish Society for Automated Image Analysis) Symposium on Image Analysis, Stockholm, Sweden, p. 17-20, 2003
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Perimeter and Area Estimations of Digitized Objects with Fuzzy Borders
Part of Proceedings of 11th International Conference on Discrete Geometry for Computer Imagery (DGCI 2003), p. 368-377, 2003
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Measuring perimeter and area in low resolution images using a fuzzy approach
Part of Proceedings of 13th Scandinavian Conference on Image Analysis (SCIA 2003), p. 853-860, 2003
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The Reconstruction of the Digital Hyperbola Segment from Its Code
Part of International Conference on Discrete Geometry for Computer Imagery, p. 159-170, 2000
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A characterization of digital disks by discrete moments
Part of International Conference on Computer Analysis of Images and Patterns, p. 582-589, 1997
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Ellipses estimation from their digitization
Part of International Conference on Discrete Geometry for Computer Imagery, p. 187-198, 1997
Conference proceedings (editor)
Manuscripts (preprints)
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Is Image-to-Image Translation the Panacea for Multimodal Image Registration? A Comparative Study
2021
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2021
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A Deep Learning based Pipeline for Efficient Oral Cancer Screening on Whole Slide Images
2019
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Fast and Robust Symmetric Image Registration Based on Intensity and Spatial Information
2018
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Sensitive key instance detection: Helping a cytotechnologist to find a needle in a haystack
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BIAFLOWS: A collaborative framework to benchmark bioimage analysis workflows
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- DOI for From Cells to Survival: Hierarchical Analysis of Cell Inter-Relations in Multiplex Microscopy for Lung Cancer Prognosis
- Download full text (pdf) of From Cells to Survival: Hierarchical Analysis of Cell Inter-Relations in Multiplex Microscopy for Lung Cancer Prognosis
Reports
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Perimeter estimation based on grey level object representation
2008
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Review of scientific papers on fuzzy shape analysis
2005
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A Brief Review on Benno Artman's "Euclid - The Creation of Mathematics"
2005
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A report on 10th Summer School on Image Processing
2002
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Reviews on Scientific Papers on Application of Fuzzy Set Theory in Image Segmentation
2002