Please head over to: https://www.uu.se/en/centre/centre-for-image-analysis/publications instead.

1. Cell Segmentation of <em>in situ </em>Transcriptomics Data using Signed Graph Partitioning. Axel Andersson, Andrea Behanova, Carolina Wählby, and Filip Malmberg. In Graph-Based Representations in Pattern Recognition, volume 14121 of Lecture Notes in Computer Science (LNCS), pp 139-148, Springer, Cham, 2023. (DOI).
2. Image Processing and Analysis Methods for Biomedical Applications. Eva Breznik. Ph.D. thesis, Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology nr 2253, Acta Universitatis Upsaliensis, Uppsala, 2023. (fulltext, preview image).
3. Dental hygienists and dentists as providers of brush biopsies for oral mucosa screening. Kristina Edman, Christina Runow Stark, Vladimir Basic, Joakim Lindblad, and Jan-Michaél Hirsch. In International Journal of Dental Hygiene, volume 21, number 3, pp 524-532, John Wiley & Sons, 2023. (DOI, Fulltext, fulltext:print).
4. Adapting Deep Learning for Microscopy: Interaction, Application, and Validation. Ankit Gupta. Ph.D. thesis, Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology nr 2321, Acta Universitatis Upsaliensis, Uppsala, 2023. (fulltext, preview image).
5. Label-free deep learning-based species classification of bacteria imaged by phase-contrast microscopy. Erik Hallström, Vinodh Kandavalli, Petter Ranefall, Johan Elf, and Carolina Wählby. In PloS Computational Biology, volume 19, number 11, Public Library of Science (PLoS), 2023. (DOI, Fulltext, fulltext:print).
6. Age-Invariant Face Recognition using Face Feature Vectors and Embedded Prototype Subspace Classifiers. Anders Hast. In Advanced Concepts for Intelligent Vision Systems, volume 14124 of Lecture Notes in Computer Science (LNCS), pp 88-99, Springer Nature, 2023. (DOI).
7. Consensus Ranking for Efficient Face Image Retrieval: A Novel Method for Maximising Precision and Recall. Anders Hast. In Image Analysis and Processing – ICIAP 2023, volume 14233 of Lecture Notes in Computer Science, pp 159-170, Springer Nature, 2023. (DOI).
8. Sex Classification of Face Images using Embedded Prototype Subspace Classifiers.. Anders Hast. In Proceedings of the 31th International Conference in Central Europe on Computer Graphics, Visualization and Computer Vision WSCG 2023, pp 43-52, Czech Republic, 2023.
9. A Study of Augmentation Methods for Handwritten Stenography Recognition. Raphaela Heil and Eva Breznik. In , 2023. (DOI).
10. Document Image Processing for Handwritten Text Recognition: Deep Learning-based Transliteration of Astrid Lindgren’s Stenographic Manuscripts. Raphaela Heil. Ph.D. thesis, Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology nr 2294, Skrifter utgivna av Svenska barnboksinstitutet nr 166, Acta Universitatis Upsaliensis, Uppsala, 2023. (fulltext, preview image).
11. Can Representation Learning for Multimodal Image Registration be Improved by Supervision of Intermediate Layers?. Elisabeth Wetzer, Joakim Lindblad, and Nataša Sladoje. In IbPRIA 2023: Pattern Recognition and Image Analysis, Lecture Notes in Computer Science, pp 261-275, Springer, 2023. (DOI, External link).
12. Partial dimensional collapse in contrastive learning when using intermediate layers. Elisabeth Wetzer, Joakim Lindblad, and Nataša Sladoje. In , 2023.
13. Representation Learning and Information Fusion: <em>Applications in Biomedical Image Processing</em>. Elisabeth Wetzer. Ph.D. thesis, Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology nr 2266, Acta Universitatis Upsaliensis, Uppsala, 2023. (fulltext, preview image).
14. INSPIRE: Intensity and Spatial Information-Based Deformable Image Registration. Johan Öfverstedt, Joakim Lindblad, and Nataša Sladoje. In PLOS ONE, volume 18, number 3, Public Library of Science (PLoS), 2023. (DOI, Fulltext, Pre-print i arXiv, fulltext:print).

1. End-to-end Multiple Instance Learning with Gradient Accumulation. Axel Andersson, Nadezhda Koriakina, Nataša Sladoje, and Joakim Lindblad. In 2022 IEEE International Conference on Big Data (Big Data), pp 2742-2746, Institute of Electrical and Electronics Engineers (IEEE), 2022. (DOI).
2. A Spatially Detailed Approach to the Assessment of Rooftop Solar Energy Potential based on LiDAR Data. Mohammad Aslani and Stefan Seipel. In GISTAM: Proceedings of the 8th International Conference on Geographical Information Systems Theory, Applications and Management, pp 56-63, SciTePress, Setúbal, 2022. (DOI, Fulltext).
3. Topology-Aware Learning for Volumetric Cerebrovascular Segmentation. Subhashis Banerjee, Dimitrios Toumpanakis, Ashis Kumar Dhara, Johan Wikström, and Robin Strand. In 2022 IEEE International Symposium on Biomedical Imaging (IEEE ISBI 2022), IEEE International Symposium on Biomedical Imaging, pp 1-4, IEEE, 2022. (DOI).
4. Efficient Parallel Thinning of 3d Objects on the Body-centered Cubic Lattice. David Brunner, Guido Brunnett, Thomas Kronfeld, and Robin Strand. In Computer-Aided Design, volume 151, Elsevier, 2022. (DOI).
5. DCNN based Oral Cancer Screening using Whole Slide Cytology Images: Effect of Increased Patch Size. Swarnadip Chatterjee, Nataša Sladoje, and Joakim Lindblad. In , 2022. (Conference information).
6. Spectral Ultrasound Imaging of Speed-of-Sound and Attenuation Using an Acoustic Mirror. Bhaskara Rao Chintada, Richard Rau, and Orcun Göksel. In Frontiers in Physics, volume 10, Frontiers Media S.A., 2022. (DOI, Fulltext, fulltext:print).
7. Patient specific deep learning based segmentation for magnetic resonance guided prostate radiotherapy. Samuel Fransson, David Tilly, and Robin Strand. In Physics and Imaging in Radiation Oncology, volume 23, pp 38-42, Elsevier, 2022. (DOI, Fulltext, fulltext:print).
8. Probabilistic spatial analysis in quantitative microscopy with uncertainty-aware cell detection using deep Bayesian regression. Alvaro Gomariz, Tiziano Portenier, Cesar Nombela-Arrieta, and Orcun Göksel. In Science Advances, volume 8, number 5, American Association for the Advancement of Science (AAAS), 2022. (DOI).
9. Unsupervised Domain Adaptation with Contrastive Learning for OCT Segmentation. Alvaro Gomariz, Huanxiang Lu, Yun Yvonna Li, Thomas Albrecht, Andreas Maunz, Fethallah Benmansour, Alessandra M. Valcarcel, Jennifer Luu, Daniela Ferrara, and Orcun Göksel. In Medical Image Computing and Computer Assisted Intervention, MICCAI 2022, pt viii, Lecture Notes in Computer Science, pp 351-361, Springer Nature, 2022. (DOI).
10. Is brightfield all you need for MoA prediction?. Ankit Gupta, Philip J Harrison, Håkan Wieslander, Jonne Rietdijk, Jordi Carreras-Puigvert, Polina Georgiev, Carolina Wählby, Ola Spjuth, and Ida-Maria Sintorn. In , 2022. (External link).
11. Towards Better Guided Attention and Human Knowledge Insertion in Deep Convolutional Neural Networks. Ankit Gupta and Ida-Maria Sintorn. In , 2022. (External link).
12. Early Detection of Oral Potentially Malignant Disorders: A Review on Prospective Screening Methods with Regard to Global Challenges. Neda Haj-Hosseini, Joakim Lindblad, Bengt Hasséus, Vinay Vijaya Kumar, Narayana Subramaniam, and Jan-Michaél Hirsch. In Journal of Maxillofacial and Oral Surgery, volume 23, number 1, pp 23-32, Springer Nature, 2022. (DOI, Fulltext, fulltext:print).
13. Magnitude of Semicircle Tiles in Fourier-space: A Handcrafted Feature Descriptor for Word Recognition using Embedded Prototype Subspace Classifiers. Anders Hast. In Journal of WSCG, volume 30, number 1-2, pp 82-90, 2022. (DOI).
14. An image registration method for voxel-wise analysis of whole-body oncological PET-CT. Hanna Jönsson, Simon Ekström, Robin Strand, Mette A Pedersen, Daniel Molin, Håkan Ahlström, and Joel Kullberg. In Scientific Reports, volume 12, Springer Nature, 2022. (DOI, Fulltext, fulltext:print).
15. MIMIR: Deep Regression for Automated Analysis of UK Biobank MRI Scans. Taro Langner, Andrés Martínez Mora, Robin Strand, Håkan Ahlström, and Joel Kullberg. In Radiology: Artificial Intelligence, volume 4, number 3, Radiological Society of North America (RSNA), 2022. (DOI).
16. Serum levels of perfluoroalkyl substances (PFAS) and body composition - A cross-sectional study in a middle-aged population. P. Monica Lind, Lars Lind, Samira Salihovic, Håkan Ahlström, Karl Michaëlsson, Joel Kullberg, and Robin Strand. In Environmental Research, volume 209, p 112677, Elsevier, 2022. (DOI, Fulltext, fulltext:print).
17. Hierarchical graph representations in digital pathology. Pushpak Pati, Guillaume Jaume, Antonio Foncubierta-Rodriguez, Florinda Feroce, Anna Maria Anniciello, Giosue Scognamiglio, Nadia Brancati, Maryse Fiche, Estelle Dubruc, Daniel Riccio, Maurizio Di Bonito, Giuseppe De Pietro, Gerardo Botti, Jean-Philippe Thiran, Maria Frucci, Orcun Göksel, and Maria Gabrani. In Medical Image Analysis, volume 75, Elsevier, 2022. (DOI, Fulltext, fulltext:print).
18. Computational analysis of subscapularis tears and pectoralis major transfers on muscular activity. Fabien Pean, Philippe Favre, and Orcun Göksel. In Clinical Biomechanics, volume 92, Elsevier, 2022. (DOI, Fulltext, fulltext:print).
19. Improved geometric accuracy of whole body diffusion-weighted imaging at 1.5T and 3T using reverse polarity gradients. Therese Sjöholm, Joel Kullberg, Robin Strand, M. Engström, Håkan Ahlström, and Filip Malmberg. In Scientific Reports, volume 12, Springer Nature, 2022. (DOI, Fulltext, fulltext:print).
20. Bioimage Data Analysis Workflows ? Advanced Components and Methods. Nataša Sladoje and Kota Miura (eds). Learning Materials in Biosciences, Springer, 2022. (DOI).
21. AI based prostate analysis system trained without human supervision to predict patient outcome from tissue samples. Peter Walhagen, Ewert Bengtsson, Maximilian Lennartz, Guido Sauter, and Christer Busch. In Journal of Pathology Informatics, 2022. (DOI, External link).
22. Cross-Sim-NGF: FFT-Based Global Rigid Multimodal Alignment of Image Volumes using Normalized Gradient Fields. Johan Öfverstedt, Joakim Lindblad, and Natasa Sladoje. In , Springer Nature, 2022. (DOI).
23. Efficient Algorithms for Global Multimodal Image Registration. Johan Öfverstedt, Joakim Lindblad, and Natasa Sladoje. In , 2022.
24. Fast computation of mutual information in the frequency domain with applications to global multimodal image alignment. Johan Öfverstedt, Joakim Lindblad, and Natasa Sladoje. In Pattern Recognition Letters, volume 159, pp 196-203, Elsevier, 2022. (DOI, Fulltext, Pre-print in arXiv, fulltext:print).
25. Methods for Reliable Image Registration: Algorithms, Distance Measures, and Representations. Johan Öfverstedt. Ph.D. thesis, Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology nr 2107, Acta Universitatis Upsaliensis, Uppsala, 2022. (fulltext, preview image).

1. Learning Whole-Slide Segmentation from Inexact and Incomplete Labels Using Tissue Graphs. Valentin Anklin, Pushpak Pati, Guillaume Jaume, Behzad Bozorgtabar, Antonio Foncubierta-Rodriguez, Jean-Philippe Thiran, Mathilde Sibony, Maria Gabrani, and Orcun Goksel. In Medical Image Computing and Computer Assisted Intervention: MICCAI 2021, volume 12902 of Lecture Notes in Computer Science (LNIP), pp 636-646, Springer Nature, Cham, 2021. (DOI, arXiv:2103.03129).
2. Word Recognition using Embedded Prototype Subspace Classifiers on a new Imbalanced Dataset. Anders Hast and Ekta Vats. In Journal of WSCG, volume 29, number 1-2, pp 39-47, University of West Bohemia, 2021. (DOI).
3. Strikethrough Removal from Handwritten Words Using CycleGANs. Raphaela Heil, Ekta Vats, and Anders Hast. In Document Analysis and Recognition -- ICDAR 2021, pp 572-586, Springer, 2021. (DOI, Fulltext, External link).
4. Icke-invasiv kontroll av cellförändringar i munslemhinnan. Jan-Michaél Hirsch, Neda Haj-Hosseini, Carina Krüger Weiner, Bengt Hasséus, and Joakim Lindblad. In Tandläkartidningen, number 9, pp 48-55, 2021. (External link).
5. The Effect of Within-Bag Sampling on End-to-End Multiple Instance Learning. Nadezhda Koriakina, Natasa Sladoje, and Joakim Lindblad. In Proceedings of the 12th International Symposium on Image and Signal Processing and Analysis (ISPA), International symposium on image and signal processing and analysis, pp 183-188, Institute of Electrical and Electronics Engineers (IEEE), 2021. (DOI).
6. Discrete Geometry and Mathematical Morphology: First International Joint Conference, DGMM 2021, Uppsala, Sweden, May 24–27, 2021, Proceedings. Joakim Lindblad, Filip Malmberg, and Natasa Sladoje (eds). Volume 12708 of Lecture Notes in Computer Science, Springer, Springer Nature Switzerland AG 2021, 2021. (DOI).
7. Image-to-Image Translation in Multimodal Image Registration: How Well Does It Work?. Jiahao Lu, Johan Öfverstedt, Joakim Lindblad, and Natasa Sladoje. In , 2021.
8. Is Image-to-Image Translation the Panacea for Multimodal Image Registration? A Comparative Study. Jiahao Lu, Johan Öfverstedt, Joakim Lindblad, and Natasa Sladoje. 2021. (External link).
9. Evaluation of in-house, haptic assisted surgical planning for virtual reduction of complex mandibular fractures. Johanna Nilsson, Fredrik Nysjö, Ingela Nyström, Johan Kämpe, and Andreas Thor. In International Journal of Computer Assisted Radiology and Surgery, volume 16, number 6, pp 1059-1068, Springer, 2021. (DOI, Fulltext, fulltext:print).
10. CytoBrowser: a browser-based collaborative annotation platform for whole slide images. Christopher Rydell and Joakim Lindblad. In F1000 Research, volume 10, F1000 Research Ltd, 2021. (DOI).
11. Computer-assisted analysis of multimodal image data—perspectives and conclusion. Natasa Sladoje, Joakim Lindblad, and Perrine Paul-Gilloteaux. In Imaging Modalities for Biological and Preclinical Research: A Compendium, Volume 2, pp III.4.g-1-III.4.g-10, Institute of Physics Publishing (IOPP), 2021. (DOI).
12. Introduction—computer-assisted analysis of multimodal image data. Natasa Sladoje and Joakim Lindblad. In Imaging Modalities for Biological and Preclinical Research: A Compendium, Volume 2, pp III.4.a-1-III.4.a-3, Institute of Physics Publishing (IOPP), 2021. (DOI).
13. Towards automatic protein co-expression quantification in immunohistochemical TMA slides. Leslie Solorzano, Carla Pereira, Diana Martins, Raquel Almeida, Fatima Carneiro, Gabriela Almeida, Carla Oliveira, and Carolina Wählby. In IEEE journal of biomedical and health informatics, volume 25, number 2, pp 393-402, Institute of Electrical and Electronics Engineers (IEEE), 2021. (DOI, Fulltext, TissUUmaps publications, fulltext:postprint, fulltext:print).
14. Contrastive Learning for Equivariant Multimodal Image Representations. Elisabeth Wetzer, Nicolas Pielawski, Eva Breznik, Johan Öfverstedt, Jiahao Lu, Carolina Wählby, Joakim Lindblad, and Natasa Sladoje. In , Cambridge University, 2021.
15. Cross-Sim-NGF: FFT-Based Global Rigid Multimodal Alignment of Image Volumes using Normalized Gradient Fields. Johan Öfverstedt, Joakim Lindblad, and Natasa Sladoje. 2021. (External link).
16. Fast Computation of Mutual Information with Application to Global Multimodal Image Alignment of Micrographs. Johan Öfverstedt, Joakim Lindblad, and Natasa Sladoje. In , 2021.

1. A fast instance selection method for support vector machines in building extraction. Mohammad Aslani and Stefan Seipel. In Applied Soft Computing, volume 97, 2020. (DOI, Fulltext, fulltext:print).
2. Adaptive Mathematical Morphology on Irregularly Sampled Signals in Two Dimensions. Teo Asplund, Cris L. Luengo Hendriks, Matthew J. Thurley, and Robin Strand. In Mathematical Morphology - Theory and Applications, volume 4, number 1, pp 108-126, Walter de Gruyter, 2020. (DOI, Fulltext, Publisher's full text, fulltext:print).
3. Uncovering hidden reasoning of convolutional neural networks in biomedical image classification by using attribution methods. Nadezhda Koriakina, Natasa Sladoje, Elisabeth Wetzer, and Joakim Lindblad. In 4th NEUBIAS Conference, Bordeaux, France, 2020.
4. Large-scale Inference of Liver Fat with Neural Networks on UK Biobank Body MRI. Taro Langner, Robin Strand, Håkan Ahlström, and Joel Kullberg. In International Conference on Medical Image Computing and Computer-Assisted Intervention (MICCAI) 2020, volume 12262 of Lecture Notes in Computer Science, pp 602-611, Springer, Cham, 2020. (DOI, Fulltext).
5. A Deep Learning Based Pipeline for Efficient Oral Cancer Screening on Whole Slide Images. Jiahao Lu, Natasa Sladoje, Christina Runow Stark, Eva Darai Ramqvist, Jan-Michaél Hirsch, and Joakim Lindblad. In Image Analysis and Recognition, Lecture Notes in Computer Science - LNCS 12132, pp 249-261, pp 249-261, Springer International Publishing, 2020. (DOI, External link).
6. Two Polynomial Time Graph Labeling Algorithms Optimizing Max-Norm-Based Objective Functions. Filip Malmberg and Krzysztof Chris Ciesielski Ciesielski. In Journal of Mathematical Imaging and Vision, volume 62, number 5, pp 737-750, 2020. (DOI).
7. Clustered Grid Cell Data Structure for Isosurface Rendering. Fredrik Nysjö. In Journal of WSCG, volume 28, number 1-2, pp 9-17, 2020. (DOI, Fulltext).
8. RayCaching: Amortized Isosurface Rendering for Virtual Reality. Fredrik Nysjö, Filip Malmberg, and Ingela Nyström. In Computer graphics forum (Print), volume 39, number 1, pp 220-230, 2020. (DOI, Fulltext, fulltext:print).
9. CoMIR: Contrastive Multimodal Image Representation for Registration. Nicolas Pielawski, Elisabeth Wetzer, Johan Öfverstedt, Jiahao Lu, Carolina Wählby, Joakim Lindblad, and Natasa Sladoje. In NeurIPS - 34th Conference on Neural Information Processing Systems, 2020. (External link, External link).
10. BIAFLOWS: A Collaborative Framework to Reproducibly Deploy and Benchmark Bioimage Analysis Workflows.. Ulysse Rubens, Romain Mormont, Lassi Paavolainen, Volker Bäcker, Benjamin Pavie, Leandro A Scholz, Gino Michiels, Martin Maška, Devrim Ünay, Graeme Ball, Renaud Hoyoux, Rémy Vandaele, Ofra Golani, Stefan G Stanciu, Natasa Sladoje, Perrine Paul-Gilloteaux, Raphaël Marée, and Sébastien Tosi. In Patterns (New York, N.Y.), volume 1, number 3, Elsevier BV, 2020. (DOI, Fulltext, fulltext:print).
11. Visualisation of 3D Property Data and Assessment of the Impact of Rendering Attributes. Stefan Seipel, Martin Andrée, Karolina Larsson, Jesper M. Paasch, and Jenny Paulsson. In Journal of Geovisualization and Spatial Analysis, volume 4, number 2, 2020. (DOI, Fulltext, fulltext:print).
12. Cross-modal Representation Learning for Efficient Registration of Multiphoton and Brightfield Microscopy Images of Skin Tissue. Elisabeth Wetzer, Nicolas Pielawski, Johan Öfverstedt, Lu Jiahao, Joakim Lindblad, A. Dumitru, M. Costache, R. Hristu, S.G. Stanciu, and Natasa Sladoje. In 4th NEUBIAS Conference, Bordeaux, France, 2020. (External link).
13. Bootstrapping Weakly Supervised Segmentation-free Word Spotting through HMM-based Alignment. Tomas Wilkinson and Carl Nettelblad. In 2020 17th International Conference on Frontiers in Handwriting Recognition (ICFHR), pp 49-54, 2020. (DOI).
14. Stochastic Distance Transform: Theory, Algorithms and Applications. Johan Öfverstedt, Joakim Lindblad, and Natasa Sladoje. In Journal of Mathematical Imaging and Vision, volume 62, pp 751-769, 2020. (DOI, Fulltext, fulltext:print).

1. Conventional analysis of movement on non-flat surfaces like the plasma membrane makes Brownian motion appear anomalous. Jeremy Adler, Ida-Maria Sintorn, Robin Strand, and Ingela Parmryd. In Communications Biology, volume 2, 2019. (DOI, Fulltext).
2. CNNs on Graphs: A New Pooling Approach and Similarities to Mathematical Morphology. Teo Asplund, Karl Bengtsson Bernander, and Eva Breznik. In , 2019.
3. Mathematical Morphology on Irregularly Sampled Data Applied to Segmentation of 3D Point Clouds of Urban Scenes. Teo Asplund, Andrés Serna, Beatriz Marcotegui, Robin Strand, and Cris L. Luengo Hendriks. In International Symposium on Mathematical Morphology and Its Applications to Signal and Image Processing, Lecture Notes In Computer Science, Springer Nature, 2019. (DOI, External link).
4. Precise Image-Based Measurements through Irregular SamplingNoggranna bildbaserade mätningar via irreguljär sampling. Teo Asplund. Ph.D. thesis, Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology nr 1869, Acta Universitatis Upsaliensis, Uppsala, 2019. (fulltext, preview image).
5. Glandular Segmentation of Prostate Cancer: An Illustration of How the Choice of Histopathological Stain Is One Key to Success for Computational Pathology. Christophe Avenel, Anna Tolf, Anca Dragomir, and Ingrid Carlbom. In Frontiers in Bioengineering and Biotechnology, volume 7, 2019. (DOI, Fulltext, fulltext:print).
6. CalligraphyNet: Augmenting handwriting generation with quill based stroke width. Kalyan Ram Ayyalasomayajula, Tomas Wilkinson, Filip Malmberg, and Anders Brun. 26th IEEE International Conference on Image Processing (Currently under review), 2019.
7. Learning based segmentation and generation methods for handwritten document images. Kalyan Ram Ayyalasomayajula. Ph.D. thesis, Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology nr 1783, Acta Universitatis Upsaliensis, Uppsala, 2019. (fulltext, preview image).
8. PDNet: Semantic segmentation integrated with a primal-dual network for document binarization. Kalyan Ram Ayyalasomayajula, Filip Malmberg, and Anders Brun. In Pattern Recognition Letters, volume 121, pp 52-60, 2019. (DOI, fulltext:postprint).
9. Image analysis in digital pathology: Combining automated assessment of Ki67 staining quality with calculation of Ki67 cell proliferation index. Ewert Bengtsson and Petter Ranefall. In Cytometry Part A, volume 95, number 7, pp 714-716, 2019. (DOI).
10. Special Section on Image Cytometry. Ewert Bengtsson and Attila Tárnok. In Cytometry Part A, volume 95A, number 4, pp 363-365, 2019. (DOI, Fulltext).
11. Oral Cancer Detection:: A Comparison of Texture Focused Deep Learning Approaches. Jo Gay, Hugo Harlin, Elisabeth Wetzer, Joakim Lindblad, and Natasa Sladoje. In Proceedings of the Swedish Society for Automated Image Analysis (SSBA), 2019. (External link).
12. Texture-based oral cancer detection: A performance analysis of deep learning approaches.. Jo Gay, Hugo Harlin, Elisabeth Wetzer, Joakim Lindblad, and Natasa Sladoje. In 3rd NEUBIAS Conference, Luxembourg, 2019.
13. Deep Learning in Image Cytometry: A Review. Anindya Gupta, Philip J. Harrison, Håkan Wieslander, Nicolas Pielawski, Kimmo Kartasalo, Gabriele Partel, Leslie Solorzano, Amit Suveer, Anna H. Klemm, Ola Spjuth, Ida-Maria Sintorn, and Carolina Wählby. In Cytometry Part A, volume 95, number 6, pp 366-380, 2019. (DOI, Fulltext, fulltext:print).
14. Creating an Atlas over Handwritten Script Signs. Anders Hast, Lasse Mårtensson, Ekta Vats, and Raphaela Heil. In Digital Humanities in the Nordic Countries, 2019.
15. Making large collections of handwritten material easily accessible and searchable. Anders Hast, Per Cullhed, Ekta Vats, and Matteo Abrate. In Digital Libraries: Supporting Open Science, volume 988 of Communications in Computer and Information Science, pp 18-28, Springer, 2019. (DOI).
16. Tracking Microscope Performance: A Workflow to Compare Point Spread Function Evaluations Over Time. Anna H. Klemm, Andreas W. Thomae, Katarina Wachal, and Steffen Dietzel. In Microscopy and Microanalysis, volume 25, number 3, pp 699-704, 2019. (DOI).
17. Visualization of convolutional neural network class activations in automated oral cancer detection for interpretation of malignancy associated changes. Nadezhda Koriakina, Natasa Sladoje, Ewert Bengtsson, Eva Darai Ramqvist, Jan M. Hirsch, Christina Runow Stark, and Joakim Lindblad. In 3rd NEUBIAS Conference, Luxembourg, 2-8 February 2019, 2019.
18. Modeling spatial correlation of transcripts with application to developing pancreas. Ruishan Liu, Marco Mignardi, Robert Jones, Martin Enge, Seung K. Kim, Stephen R. Quake, and James Zou. In Scientific Reports, volume 9, 2019. (DOI, Fulltext).
19. A Deep Learning based Pipeline for Efficient Oral Cancer Screening on Whole Slide Images. Jiahao Lu, Natasa Sladoje, Christina Runow Stark, Eva Darai Ramqvist, Jan-Michael Hirsch, and Joakim Lindblad. 2019. (arXiv:1910.10549).
20. On the Effectiveness of Generative Adversarial Networks as HEp-2 Image Augmentation Tool. Tomáš Majtner, Buda Baji?, Joakim Lindblad, Natasa Sladoje, Victoria Blanes-Vidal, and Esmaeil S. Nadimi. In Scandinavian Conference on Image Analysis: SCIA 2019, volume 11482 of Lecture Notes in Computer Science, pp 439-451, 2019. (DOI, External link).
21. Optimization of max-norm objective functions in image processing and computer vision. Filip Malmberg, Krzysztof Chris Ciesielski, and Robin Strand. In Discrete Geometry for Computer Imagery, volume 11414 of Lecture Notes in Computer Science, pp 206-218, Springer, 2019. (DOI).
22. Image and Data Analysis for Biomedical Quantitative Microscopy. Damian J. Matuszewski. Ph.D. thesis, Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology nr 1864, Acta Universitatis Upsaliensis, Uppsala, 2019. (fulltext, preview image).
23. Bioimage Data Analysis Workflows. Kota Miura and Natasa Sladoje (eds). Learning Materials in Biosciences, Springer, 2019. (DOI, Fulltext, fulltext).
24. In search of the scribe: Letter spotting as a tool for identifying scribes in large handwritten text corpora. Lasse Mårtensson, Ekta Vats, Anders Hast, and Alicia Fornés. In Human IT, volume 14, number 2, pp 95-120, 2019. (External link).
25. Distance Transform Based on Weight Sequences. Benedek Nagy, Robin Strand, and Nicolas Normand. In DGCI 2019: Discrete Geometry for Computer Imagery, volume 11414 of Lecture Notes in Computer Science, pp 62-74, Springer, Switzerland AG, 2019. (DOI, External link).
26. Rational nanotoolbox with theranostic potential for medicated pro-regenerative corneal implants. Hirak K. Patra, Mohammad Azharuddin, Mohammad M. Islam, Georgia Papapavlou, Suryyani Deb, Johannes Osterrieth, Geyunjian Harry Zhu, Thobias Romu, Ashis Kumar Dhara, Mohammad J. Jafari, Amineh Gadheri, Jorma Hinkula, Madhavan S. Rajan, and Nigel K. H. Slater. In Advanced Functional Materials, volume 29, number 38, 2019. (DOI).
27. Average volume reference space for large scale registration of whole-body magnetic resonance images. Martino Pilia, Joel Kullberg, Håkan Ahlström, Filip Malmberg, Simon Ekström, and Robin Strand. In PLOS ONE, volume 14, number 10, 2019. (DOI, Fulltext, fulltext:print).
28. Region-by-region analysis of PET, MRI, and histology in en bloc-resected oligodendrogliomas reveals intra-tumoral heterogeneity. Kenney Roy Roodakker, Ali Alhuseinalkhudhur, Mohammed Al-Jaff, Maria Georganaki, Maria Zetterling, Shala G. Berntsson, Torsten Danfors, Robin Strand, Per-Henrik Edqvist, Anna Dimberg, Elna-Marie Larsson, and Anja Smits. In European Journal of Nuclear Medicine and Molecular Imaging, volume 46, number 3, pp 569-579, 2019. (DOI, Fulltext).
29. A strategy for OCT estimation of the optic nerve head pigment epithelium central limit-inner limit of the retina minimal distance, PIMD-2?. Camilla Sandberg Melin, Filip Malmberg, and Per G. Söderberg. In Acta Ophthalmologica, volume 97, number 2, pp 208-213, 2019. (DOI).
30. Facilitating Ultrastructural Pathology through Automated Imaging and Analysis. Ida-Maria Sintorn, Amit Suveer, Anca Dragomir, Kjell Hultenby, Elisabeth Wetzer, Kristína Lidayová, Nataša Sladoje, Joakim Lindblad, and Martin Ryner. In Journal of Pathology Informatics, volume 10, number 1, pp 38-39, Elsevier, 2019. (Abstracts in full-text).
31. A whole-body FDG PET/MR atlas for multiparametric voxel-based analysis. Therese Sjöholm, Simon Ekström, Robin Strand, Håkan Ahlström, Lars Lind, Filip Malmberg, and Joel Kullberg. In Scientific Reports, volume 9, 2019. (DOI, Fulltext, fulltext:print).
32. Methods for Processing and Analysis of Biomedical TEM Images. Amit Suveer. Ph.D. thesis, Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology nr 1807, Acta Universitatis Upsaliensis, Uppsala, 2019. (fulltext, preview image).
33. New De?nition of Quality-Scale Robustness for Image Processing Algorithms, with Generalized Uncertainty Modeling, Applied to Denoising and Segmentation. Antoine Vacavant, Marie-Ange Lebre, Hugo Rositi, Manuel Grand-Brochier, and Robin Strand. In RRPR 2018: Reproducible Research in Pattern Recognition: Reproducible Research in Pattern Recognition, volume 11455 of Lecture Notes in Computer Science, pp 138-149, Springer, Switzerland AG, 2019. (DOI, External link).
34. Training-Free and Segmentation-Free Word Spotting using Feature Matching and Query Expansion. Ekta Vats, Anders Hast, and Alicia Fornés. In Proc. 15th International Conference on Document Analysis and Recognition, 2019. (External link).
35. Correcting exorbitism by monobloc frontofacial advancement in Crouzon–Pfeiffer syndrome: An age-specific, time-related, controlled study. Benjamin L. M. Way, Roman H. Khonsari, Tharsika Karunakaran, Johan Nysjö, Ingela Nyström, David J. Dunaway, Robert D. Evans, Richard D. Hayward, and Jonathan A. Britto. In Plastic and reconstructive surgery (1963), volume 143, number 1, pp 121e-132e, 2019. (DOI).
36. Towards automated multiscale Glomeruli detection and analysis in TEM by fusion of CNN and LBP maps. Elisabeth Wetzer, Joakim Lindblad, Ida-Maria Sintorn, Kjell Hultenby, and Natasa Sladoje. In 3rd NEUBIAS Conference, Luxembourg, 2019. (External link).
37. Towards automated multiscale imaging and analysis in TEM: Glomerulus detection by fusion of CNN and LBP maps. Elisabeth Wetzer, Joakim Lindblad, Ida-Maria Sintorn, Kjell Hultenby, and Natasa Sladoje. In Computer Vision: ECCV 2018 Workshops, volume 11134 of Lecture Notes in Computer Sciences (LNCS), pp 465-475, Springer, Cham, 2019. (DOI, Conference website).
38. Learning based Word Search and Visualisation for Historical Manuscript Images. Tomas Wilkinson. Ph.D. thesis, Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology nr 1798, Acta Universitatis Upsaliensis, Uppsala, 2019. (fulltext, preview image).
39. Visual Saliency: From Pixel-Level to Object-Level Analysis. Jianming Zhang, Filip Malmberg, and Stan Sclaroff. Springer, 2019. (DOI).
40. Fast and Robust Symmetric Image Registration Based on Distances Combining Intensity and Spatial Information. Johan Öfverstedt, Joakim Lindblad, and Natasa Sladoje. In IEEE Transactions on Image Processing, volume 28, number 7, pp 3584-3597, IEEE, 2019. (DOI, Fulltext, fulltext:print).
41. Stochastic Distance Functions with Applications in Object Detection and Image Segmentation. Johan Öfverstedt, Joakim Lindblad, and Natasa Sladoje. In Swedish Symposium on Image Analysis, 2019. (External link).
42. Stochastic Distance Transform. Johan Öfverstedt, Joakim Lindblad, and Natasa Sladoje. In Discrete Geometry for Computer Imagery, volume 11414 of Lecture Notes in Computer Science, pp 75-86, Springer, 2019. (DOI, External link).

1. Denoising of short exposure transmission electron microscopy images for ultrastructural enhancement. Buda Bajic, Amit Suveer, Anindya Gupta, Ivana Pepic, Joakim Lindblad, Natasa Sladoje, and Ida-Maria Sintorn. In Proc. 15th International Symposium on Biomedical Imaging, pp 921-925, IEEE, 2018. (DOI).
2. Detection of Malignancy-Associated Changes Due to Precancerous and Oral Cancer Lesions: A Pilot Study Using Deep Learning. Ewert Bengtsson, Håkan Wieslander, Gustav Forslid, Carolina Wählby, Jan-Michael Hirsch, Christina Runow Stark, Sajith Kecheril Sadanandan, and Joakim Lindblad. In CYTO2018, 2018. (External link).
3. SoftCut:: A Virtual Planning Tool for Soft Tissue Resection on CT Images. Ludovic Blache, Fredrik Nysjö, Filip Malmberg, Andreas Thor, Andres Rodriguez-Lorenzo, and Ingela Nyström. In Medical Image Understanding and Analysis, Communications in Computer and Information Science, pp 299-310, Springer, Cham, 2018. (DOI, External link).
4. The Scarcity of Universal Colour Names. Gunilla Borgefors. In Proceedings of 7th International Conference on Pattern Recognition Applications and Methods (ICPRAM 2018), pp 496-502, SciTePress, 2018. (DOI).
5. Interactive segmentation of glioblastoma for post-surgical treatment follow-up. Ashis Kumar Dhara, Erik Arids, Markus Fahlström, Johan Wikström, Elna-Marie Larsson, and Robin Strand. In Proc. 24th International Conference on Pattern Recognition, pp 1199-1204, IEEE, 2018. (DOI).
6. The Effect of DMPA Use on the Human Cervical Epithelium: Mechanisms Revealed by Image Analysis. Gabriella Edfeldt, Julie Lajoie, Maria Röhl, Kenneth Omollo, Carolina Wählby, Genevieve Boily-Larouche, Joshua Kimani, Keith Fowke, Kristina Broliden, and Annelie Tjernlund. In AIDS Research and Human Retroviruses, volume 34, number S1, pp 310-310, 2018. (Abstracts).
7. Human Immunodeficiency Virus-Infected Women Have High Numbers of CD103^-CD8⁺ T Cells Residing Close to the Basal Membrane of the Ectocervical Epithelium. Anna Gibbs, Marcus Buggert, Gabriella Edfeldt, Petter Ranefall, Andrea Introini, Stanley Cheuk, Elisa Martini, Liv Eidsmo, Terry B. Ball, Joshua Kimani, Rupert Kaul, Annika C. Karlsson, Carolina Wählby, Kristina Broliden, and Annelie Tjernlund. In Journal of Infectious Diseases, volume 218, number 3, pp 453-465, 2018. (DOI).
8. Automatic detection of multisize pulmonary nodules in CT images: Large-scale validation of the false-positive reduction step. Anindya Gupta, Tonis Saar, Olev Martens, and Yannick Le Moullec. In Medical physics (Lancaster), volume 45, number 3, pp 1135-1149, 2018. (DOI).
9. Denoising of Short Exposure Transmission Electron Microscopy Images using CNN. Anindya Gupta, Amit Suveer, Buda Bajic, Ivana Pepic, Joakim Lindblad, Natasa Sladoje, and Ida-Maria Sintorn. In Swedish Symposium on Image Analysis, 2018. (External link).
10. <em>TexT</em> – Text extractor tool for handwritten document transcription and annotation. Anders Hast, Per Cullhed, and Ekta Vats. In Digital Libraries and Multimedia Archives, volume 806 of Communications in Computer and Information Science, pp 81-92, Springer, 2018. (DOI).
11. A fast Fourier based feature descriptor and a cascade nearest neighbour search with an efficient matching pipeline for mosaicing of microscopy images. Anders Hast, Victoria A. Sablina, Ida-Maria Sintorn, and Gustaf Kylberg. In Pattern Recognition and Image Analysis, volume 28, number 2, pp 261-272, 2018. (DOI).
12. An intelligent user interface for efficient semi-automatic transcription of historical handwritten documents. Anders Hast and Ekta Vats. In Proc. 23rd International Conference on Intelligent User Interfaces Companion, ACM Press, New York, 2018. (DOI).
13. Radial line Fourier descriptor for historical handwritten text representation. Anders Hast and Ekta Vats. In Proc. 26th International Conference on Computer Graphics: Visualization and Computer Vision, 2018. (Proceedings).
14. Radial line Fourier descriptor for historical handwritten text representation. Anders Hast and Ekta Vats. In Journal of WSCG, volume 26, number 1, pp 31-40, 2018. (DOI).
15. Exploring the Applicability of Capsule Networks for WordSpotting in Historical Handwritten Manuscripts. Raphaela Heil, Ekta Vats, and Anders Hast. In , 2018.
16. Word Spotting in Historical Handwritten Manuscripts using Capsule Networks. Raphaela Heil, Ekta Vats, and Anders Hast. In , 2018.
17. Multiplexed fluorescence microscopy reveals heterogeneity among stromal cells in mouse bone marrow sections. Karolin Holzwarth, Ralf Köhler, Lars Philipsen, Koji Tokoyoda, Valeriia Ladyhina, Carolina Wählby, Raluca A. Niesner, and Anja E. Hauser. In Cytometry Part A, volume 93, number 9, pp 876-888, 2018. (DOI).
18. Localization of lung fields in HRCT images using a deep convolution neural network. Abhishek Kumar, Sunita Agarwala, Ashis Kumar Dhara, Sudipta Mukhopadhyay, Debashis Nandi, Mandeep Garg, Niranjan Khandelwal, and Naveen Kalra. In Medical Imaging 2018: Computer-Aided Diagnosis, volume 10575 of Proc. SPIE, pp 1057535:1-8, Bellingham, WA, 2018. (DOI).
19. When Can lp-norm Objective Functions Be Minimized via Graph Cuts?. Filip Malmberg and Robin Strand. In Combinatorial Image Analysis, Lecture Notes in Computer Science, pp 112-117, Springer, 2018. (DOI, External link).
20. Image-Based Detection of Patient-Specific Drug-Induced Cell-Cycle Effects in Glioblastoma. Damian J. Matuszewski, Carolina Wählby, Cecilia Krona, Sven Nelander, and Ida-Maria Sintorn. In SLAS Discovery, volume 23, number 10, pp 1030-1039, 2018. (DOI).
21. Minimal annotation training for segmentation of microscopy images. Damian J. Matuszewski and Ida-Maria Sintorn. In Proc. 15th International Symposium on Biomedical Imaging, pp 387-390, IEEE, 2018. (DOI).
22. Finish line distinctness and accuracy in 7 intraoral scanners versus conventional impression: an in vitro descriptive comparison. Robert Nedelcu, Pontus Olsson, Ingela Nyström, and Andreas Thor. In BMC Oral Health, volume 18, 2018. (DOI, Fulltext).
23. Comparison analysis of orbital shape and volume in unilateral fractured orbits. Johanna Nilsson, Johan Nysjö, Anders-Petter Carlsson, and Andreas Thor. In Journal of Cranio-Maxillofacial Surgery, volume 46, number 3, pp 381-387, 2018. (DOI).
24. Brush Biopsy For HR-HPV Detection With FTA Card And AI For Cytology Analysis - A Viable Non-invasive Alternative. Christina Runow Stark, Inger M. Gustavsson, Ulf B. Gyllensten, Eva Darai Ramqvist, Joakim Lindblad, Carolina Wählby, Ewert Bengtsson, and Jan M. Hirsch. In EAOM2018, 2018.
25. Learning surrogate models of document image quality metrics for automated document image processing. Prashant Singh, Ekta Vats, and Anders Hast. In Proc. 13th IAPR International Workshop on Document Analysis Systems, pp 67-72, IEEE, 2018. (DOI).
26. Whole Slide Image Registration for the Study of Tumor Heterogeneity. Leslie Solorzano, Gabriela Almeida, Bárbara Mesquita, Diana Martins, Carla Oliveira, and Carolina Wählby. In MICCAI 2018 - International Workshop on Ophthalmic Medical Image Analysis: OMIA 2018, COMPAY 2018: Computational Pathology and Ophthalmic Medical Image Analysis, volume 11039 of Lecture Notes in Computer Science (LNCS), pp 95-102, Springer, Cham, 2018. (DOI, External link).
27. An Objective Scoring Framework for Histology Slide Image Mosaics Applicable for the Reliable Benchmarking of Image Quality Assessment Algorithms. Tiberiu Totu, Roxana Buga, Adrian Dumitru, Mariana Costache, Natasa Sladoje, and Stefan Stanciu. In IEEE Access, volume 6, pp 53080-53091, IEEE, 2018. (DOI).
28. Extracting script features from a large corpus of handwritten documents. Ekta Vats, Anders Hast, and Lasse Mårtensson. In Digital Humanities in the Nordic Countries: Book of Abstracts, 2018. (Abstracts).
29. Towards automated multiscale imaging and analysis in TEM: Glomeruli detection by fusion of CNN and LBP maps. Elisabeth Wetzer, Joakim Lindblad, Ida-Maria Sintorn, Kjell Hultenby, and Natasa Sladoje. In Swedish Symposium on Deep Learning, 2018. (External link).
30. Quantitative image analysis of protein expression and colocalisation in skin sections. Hanqian Zhang, Maja Ericsson, Marie Virtanen, Simone Weström, Carolina Wählby, Anders Vahlquist, and Hans Törmä. In Experimental dermatology, volume 27, number 2, pp 196-199, 2018. (DOI).
31. Distance Between Vector-valued Images based on Intersection Decomposition with Applications in Object Detection. Johan Öfverstedt, Natasa Sladoje, and Joakim Lindblad. In Swedish Symposium on Image Analysis, 2018. (External link).
32. Fast and Robust Symmetric Image Registration Based on Intensity and Spatial Information. Johan Öfverstedt, Joakim Lindblad, and Natasa Sladoje. 2018. (External link).

1. Automated segmentation of lung field in HRCT images using active shape model. Sunita Agarwala, Debashis Nandi, Abhishek Kumar, Ashis Kumar Dhara, Sumitra Basu Thakur, Anup Sadhu, and Ashok Kumar Bhadra. In Proc. 37th Region 10 Conference, pp 2516-2520, IEEE, 2017. (DOI).
2. Mathematical morphology on irregularly sampled data in one dimension. Teo Asplund, Cris L. Luengo Hendriks, Matthew J. Thurley, and Robin Strand. In Mathematical Morphology - Theory and Applications, volume 2, number 1, pp 1-24, 2017. (DOI, Fulltext).
3. Document Binarization Combining with Graph Cuts and Deep Neural Networks. Kalyan Ram Ayyalasomayajula and Anders Brun. In , 2017. (fulltext:postprint).
4. Historical document binarization combining semantic labeling and graph cuts. Kalyan Ram Ayyalasomayajula and Anders Brun. In Image Analysis: Part I, volume 10269 of Lecture Notes in Computer Science, pp 386-396, Springer, 2017. (DOI, fulltext:postprint).
5. Semantic Labeling using Convolutional Networks coupled with Graph-Cuts for Document binarization. Kalyan Ram Ayyalasomayajula and Anders Brun. In , 2017. (fulltext:postprint).
6. Progress in Pattern Recognition, Image Analysis, Computer Vision, and Applications. César Beltrán-Castañón, Ingela Nyström, and Fazel Famili (eds). Volume 10125 of Lecture Notes in Computer Science, Springer, 2017. (DOI).
7. Computer-aided diagnostics in digital pathology. Ewert Bengtsson, Håvard Danielsen, Darren Treanor, Metin N. Gurcan, Calum MacAulay, and Béla Molnár. In Cytometry Part A, volume 91, number 6, pp 551-554, 2017. (DOI).
8. Image processing and its hardware support: Analysis vs synthesis - historical trends. Ewert Bengtsson. In Image Analysis, SCIA 2017, Pt I, pp 3-14, Switzerland, 2017. (DOI).
9. A web application to analyse and visualize digital images at multiple resolutions. Maxime Bombrun, Petter Ranefall, and Carolina Wählby. In , 2017.
10. Decoding gene expression in 2D and 3D. Maxime Bombrun, Petter Ranefall, Joakim Lindblad, Amin Allalou, Gabriele Partel, Leslie Solorzano, Xiaoyan Qian, Mats Nilsson, and Carolina Wählby. In Image Analysis: Part II, volume 10270 of Lecture Notes in Computer Science, pp 257-268, Springer, 2017. (DOI, fulltext:postprint).
11. Quantitative high-content/high-throughput microscopy analysis of lipid droplets in subject-specific adipogenesis models. Maxime Bombrun, Hui Gao, Petter Ranefall, Niklas Mejhert, Peter Arner, and Carolina Wählby. In Cytometry Part A, volume 91, number 11, pp 1068-1077, 2017. (DOI).
12. Hormonal contraceptive use affects HIV susceptibility: mechanisms revealed by image analysis. Gabriella Edfeldt, Julie Lajoie, Maria Röhl, Annelie Tjernlund, Carolina Wählby, Kenneth Odiwuor Omollo, Genevieve Boily-Larouche, Julianna Cheruiyot, Makubo Kimani, Joshua Kimani, Julius Oyugi, Keith R. Fowke, and Kristina Broliden. In Scandinavian Journal of Immunology, volume 86, number 4, pp 281-281, 2017. (DOI).
13. Single-cell analysis of human pancreas reveals transcriptional signatures of aging and somatic mutation patterns. Martin Enge, H. Efsun Arda, Marco Mignardi, John Beausang, Rita Bottino, Seung K. Kim, and Stephen R. Quake. In Cell, volume 171, number 2, pp 321-330.e14, 2017. (DOI).
14. Osteochondrosis, Synovial Fossae, and Articular Indentations in the Talus and Distal Tibia of Growing Domestic Pigs and Wild Boars. P. E. Etterlin, S. Ekman, Robin Strand, K. Olstad, and C. J. Ley. In Veterinary pathology, volume 54, number 3, pp 445-456, 2017. (DOI).
15. Increased numbers of CD103^-CD8⁺ T_RM cells in the cervical mucosa of HIV-infected women. Anna Gibbs, Marcus Buggert, Gabriella Edfeldt, Petter Ranefall, Andrea Introini, Stanley Cheuk, Elisa Martini, Liv Eidsmo, Taha Hirbod, Terry B. Ball, Joshua Kimani, Rupert Kaul, Annika C. Karlsson, Carolina Wählby, Kristina Broliden, and Annelie Tjernlund. In Scandinavian Journal of Immunology, volume 86, number 4, pp 288-289, 2017. (DOI).
16. Convolutional neural networks for false positive reduction of automatically detected cilia in low magnification TEM images. Anindya Gupta, Amit Suveer, Joakim Lindblad, Anca Dragomir, Ida-Maria Sintorn, and Nataša Sladoje. In Image Analysis: Part I, volume 10269 of Lecture Notes in Computer Science, pp 407-418, Springer, 2017. (DOI).
17. False positive reduction of cilia detected in low resolution TEM images using a convolutional neural network. Anindya Gupta, Amit Suveer, Joakim Lindblad, Anca Dragomir, Ida-Maria Sintorn, and Natasa Sladoje. In Swedish Symposium on Image Analysis, Swedish Society for Automated Image Analysis, 2017. (fulltext:print).
18. An efficient descriptor based on radial line integration for fast non invariant matching and registration of microscopy images. Anders Hast, Gustav Kylberg, and Ida-Maria Sintorn. In Advanced Concepts for Intelligent Vision Systems, volume 10617 of Lecture Notes in Computer Science, pp 723-734, Springer, 2017. (DOI).
19. Deep Fish: Deep Learning-Based Classification of Zebrafish Deformation for High-Throughput Screening. Omer Ishaq, Sajith Kecheril Sadanandan, and Carolina Wählby. In Journal of Biomolecular Screening, volume 22, number 1, pp 102-107, 2017. (DOI).
20. Automated training of deep convolutional neural networks for cell segmentation. Sajith Kecheril Sadanandan, Petter Ranefall, Sylvie Le Guyader, and Carolina Wählby. In Scientific Reports, volume 7, 2017. (DOI, Fulltext, fulltext:print).
21. Spheroid segmentation using multiscale deep adversarial networks. Sajith Kecheril Sadanandan, Johan Karlsson, and Carolina Wählby. In IEEE International Conference on Computer Vision, IEEE International Conference on Computer Vision Workshops, IEEE, 2017. (DOI).
22. Airway-tree segmentation in subjects with acute respiratory distress syndrome. Kristína Lidayová, Duván Alberto Gómez Betancur, Hans Frimmel, Marcela Hernández Hoyos, Maciej Orkisz, and Örjan Smedby. In Image Analysis: Part II, volume 10270 of Lecture Notes in Computer Science, pp 76-87, Springer, 2017. (DOI).
23. Classification of cross-sections for vascular skeleton extraction using convolutional neural networks. Kristína Lidayová, Anindya Gupta, Hans Frimmel, Ida-Maria Sintorn, Ewert Bengtsson, and Örjan Smedby. In Medical Image Understanding and Analysis, volume 723 of Communications in Computer and Information Science, pp 182-194, Springer, 2017. (DOI).
24. Fast Methods for Vascular Segmentation Based on Approximate Skeleton Detection. Kristína Lidayová. Ph.D. thesis, Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology nr 1496, Acta Universitatis Upsaliensis, Uppsala, 2017. (fulltext, preview image).
25. Improved centerline tree detection of diseased peripheral arteries with a cascading algorithm for vascular segmentation. Kristína Lidayová, Hans Frimmel, Ewert Bengtsson, and Örjan Smedby. In Journal of Medical Imaging, volume 4, pp 024004:1-11, 2017. (DOI).
26. On the precision of third person perspective augmented reality for target designation tasks. Fei Liu and Stefan Seipel. In Multimedia tools and applications, volume 76, number 14, pp 15279-15296, 2017. (DOI, Fulltext, fulltext:print).
27. Automated segmentation of human cervical-supraclavicular adipose tissue in magnetic resonance images. Elin Lundström, Robin Strand, Anders Forslund, Peter Bergsten, Daniel Weghuber, Håkan Ahlström, and Joel Kullberg. In Scientific Reports, volume 7, 2017. (DOI, Fulltext, fulltext:print).
28. Exact Evaluation of Targeted Stochastic Watershed Cuts. Filip Malmberg, Cris L. Luengo Hendriks, and Robin Strand. In Discrete Applied Mathematics, volume 216, number 2, pp 449-460, Elsevier, 2017. (DOI).
29. The Boolean Map Distance: Theory and Efficient Computation. Filip Malmberg, Robin Strand, Jianming Zhang, and Stan Sclaroff. In International Conference on Discrete Geometry for Computer Imagery, volume 10502 of Lecture notes in computer science, pp 335-346, Springer, 2017. (DOI).
30. Bridging Histology and Bioinformatics: Computational analysis of spatially resolved transcriptomics. Marco Mignardi, Omer Ishaq, Xiaoyan Qian, and Carolina Wählby. In Proceedings of the IEEE, volume 105, number 3, pp 530-541, 2017. (DOI, Fulltext).
31. Using anti-aliased signed distance fields for generating surgical guides and plates from CT images. Fredrik Nysjö, Pontus Olsson, Filip Malmberg, Ingrid B. Carlbom, and Ingela Nyström. In Journal of WSCG, volume 25, number 1, pp 11-20, 2017. (Fulltext, fulltext:print).
32. BoneSplit – A 3D painting tool for interactive bone segmentation in CT images. Ingela Nyström, Johan Nysjö, Andreas Thor, and Filip Malmberg. In Pattern Recognition and Information Processing: PRIP 2016, volume 673 of Communications in Computer and Information Science, pp 3-13, Springer, 2017. (DOI).
33. Deep Neural Networks and Image Analysis for Quantitative Microscopy. Sajith Kecheril Sadanandan. Ph.D. thesis, Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology nr 1566, Acta Universitatis Upsaliensis, Uppsala, 2017. (fulltext, preview image).
34. Skeletonization: Theory, Methods, and Applications. Punam K. Saha, Gunilla Borgefors, and Gabriella Sanniti di Baja (eds). Computer Vision and Pattern Recognition, Academic Press, London, 2017. (DOI).
35. Skeletonization and its applications – a review. Punam K. Saha, Gunilla Borgefors, and Gabriella Sanniti di Baja. In Skeletonization: Theory, Methods, and Applications, Computer Vision and Pattern Recognition, pp 3-42, Academic Press, London, 2017. (DOI).
36. Differential neuroprotective effects of interleukin-1 receptor antagonist on spinal cord neurons after excitotoxic injury. Nikos Schizas, Sharn Perry, Brittmarie Andersson, Carolina Wählby, Klas Kullander, and Nils Hailer. In Neuroimmunomodulation, volume 24, pp 220-230, 2017. (DOI).
37. Distance Between Vector-Valued Representations of Objects in Images with Application in Object Detection and Classification. Natasa Sladoje and Joakim Lindblad. In In Proc. of the 18th International Workshop on Combinatorial Image Analysis, IWCIA2017, volume 10256 of Lecture Notes in Computer Science, pp 243-255, Springer, 2017. (DOI).
38. A concept for holistic whole body MRI data analysis, Imiomics. Robin Strand, Filip Malmberg, Lars Johansson, Lars Lind, Magnus Sundbom, Håkan Ahlström, and Joel Kullberg. In PLOS ONE, volume 12, number 2, 2017. (DOI, Fulltext, fulltext:print).
39. Cilia ultrastructural visibility enhancement by multiple instance registration and super-resolution reconstruction. Amit Suveer, Natasa Sladoje, Joakim Lindblad, Anca Dragomir, and Ida-Maria Sintorn. In Swedish Symposium on Image Analysis, Swedish Society for Automated Image Analysis, 2017.
40. Enhancement of cilia sub-structures by multiple instance registration and super-resolution reconstruction. Amit Suveer, Nataša Sladoje, Joakim Lindblad, Anca Dragomir, and Ida-Maria Sintorn. In Image Analysis: Part II, volume 10270 of Lecture Notes in Computer Science, pp 362-374, Springer, 2017. (DOI).
41. Further analysis of clinical feasibility of OCT-based glaucoma diagnosis with Pigment epithelium central limit–Inner limit of the retina Minimal Distance (PIMD). Per G. Söderberg, Filip Malmberg, and Camilla Sandberg Melin. In Ophthalmic Technologies XXVII, volume 10045 of Proc. SPIE, SPIE - International Society for Optical Engineering, Bellingham, WA, 2017. (DOI).
42. Objective automated quantification of fluorescence signal in histological sections of rat lens. Nooshin Talebizadeh, Nanna Zhou Hagström, Zhaohua Yu, Martin Kronschläger, Per Söderberg, and Carolina Wählby. In Cytometry Part A, volume 91, number 8, pp 815-821, 2017. (DOI).
43. Automatic document image binarization using Bayesian optimization. Ekta Vats, Anders Hast, and Prashant Singh. In Proc. 4th International Workshop on Historical Document Imaging and Processing, pp 89-94, ACM Press, New York, 2017. (DOI).
44. On-the-fly historical handwritten text annotation. Ekta Vats and Anders Hast. In Proc. 14th IAPR International Conference on Document Analysis and Recognition, pp 10-14, IEEE, 2017. (DOI).
45. Deep convolutional neural networks for detecting cellular changes due to malignancy. Håkan Wieslander, Gustav Forslid, Ewert Bengtsson, Carolina Wählby, Jan-Michaél Hirsch, Christina Runow Stark, and Sajith Kecheril Sadanandan. In Proc. 16th International Conference on Computer Vision Workshops, pp 82-89, IEEE Computer Society, 2017. (DOI).
46. Neural Ctrl-F: Segmentation-free query-by-string word spotting in handwritten manuscript collections. Tomas Wilkinson, Jonas Lindström, and Anders Brun. In 2017 IEEE International Conference on Computer Vision (ICCV), IEEE International Conference on Computer Vision, pp 4443-4452, IEEE, 2017. (DOI, fulltext:postprint).
47. Neural Ctrl-F: Segmentation-free Query-by-String Word Spotting in Handwritten Manuscript Collections. Tomas Wilkinson, Jonas Lindström, and Anders Brun. In , 2017.
48. Distance between vector-valued fuzzy sets based on intersection decomposition with applications in object detection. Johan Öfverstedt, Natasa Sladoje, and Joakim Lindblad. In Mathematical Morphology and its Applications to Signal and Image Processing, volume 10225 of Lecture Notes in Computer Science, pp 395-407, Springer, 2017. (DOI).

1. A Faster, Unbiased Path Opening by Upper Skeletonization and Weighted Adjacency Graphs. Teo Asplund and Cris L. Luengo Hendriks. In IEEE Transactions on Image Processing, volume 25, number 12, pp 5589-5600, 2016. (DOI).
2. Solving the Table Maker's Dilemma on current SIMD architectures. Christophe Avenel, Pierre Fortin, Mourad Gouicem, and Samia Zaidi. In Scalable computing: Practice and Experience, volume 17, number 3, pp 237-250, 2016. (DOI).
3. Feature evaluation for handwritten character recognition with regressive and generative Hidden Markov Models. Kalyan Ram Ayyalasomayajula, Carl Nettelblad, and Anders Brun. In Advances in Visual Computing: Part I, volume 10072 of Lecture Notes in Computer Science, pp 278-287, Springer, 2016. (DOI, fulltext:postprint).
4. Blind deconvolution of images degraded with mixed Poisson-Gaussian noise with application in Transmission Electron Microscopy. Buda Bajic, Joakim Lindblad, and Nataša Sladoje. In Proceedings of the Swedish Society for Automated Image Analysis, pp 137-141, Uppsala, 2016.
5. Blind restoration of images degraded with mixed poisson-Gaussian noise with application in transmission electron microscopy. Buda Bajic, Joakim Lindblad, and Nataša Sladoje. In 2016 Ieee 13Th International Symposium On Biomedical Imaging (ISBI), IEEE International Symposium on Biomedical Imaging, pp 123-127, IEEE, 2016. (DOI).
6. Restoration of images degraded by signal-dependent noise based on energy minimization: an empirical study. Buda Bajic, Joakim Lindblad, and Nataša Sladoje. In Journal of Electronic Imaging (JEI), volume 25, number 4, 2016. (DOI, Fulltext, fulltext:print).
7. Single image super-resolution reconstruction in presence of mixed Poisson-Gaussian noise. Buda Bajic, Joakim Lindblad, and Natasa Sladoje. In 2016 SIXTH INTERNATIONAL CONFERENCE ON IMAGE PROCESSING THEORY, TOOLS AND APPLICATIONS (IPTA), International Conference on Image Processing Theory Tools and Applications, IEEE, 2016. (DOI).
8. A chronological and mathematical overview of digital circle generation algorithms: Introducing efficient 4- and 8-connected circles. Tony Barrera, Anders Hast, and Ewert Bengtsson. In International Journal of Computer Mathematics, volume 93, number 8, pp 1241-1253, 2016. (DOI).
9. TissueMaps: A large multi-scale data analysis platform for digital image application built on open-source software. Maxime Bombrun, Petter Ranefall, and Carolina Wählby. In , 2016.
10. Extracting fiber and network connectivity data using microtomography images of paper. Svetlana Borodulina, Erik L. G. Wernersson, Artem Kulachenko, and Cris L. Luengo Hendriks. In Nordic Pulp & Paper Research Journal, volume 31, number 3, pp 469-478, 2016. (DOI).
11. Preconditioning 2D integer data for fast convex hull computations. José Oswaldo Cadenas, Graham M. Megson, and Cris L. Luengo Hendriks. In PLOS ONE, volume 11, number 3, 2016. (DOI, Fulltext).
12. Comparison of 2D radiography and a semi-automatic CT-based 3D method for measuring change in dorsal angulation over time in distal radius fractures. Albert Christersson, Johan Nysjö, Lars Berglund, Filip Malmberg, Ida-Maria Sintorn, Ingela Nyström, and Sune Larsson. In Skeletal Radiology, volume 45, number 6, pp 763-769, 2016. (DOI).
13. A new method for reconstructing brain morphology: Applying the brain-neurocranial spatial relationship in an extant lungfish to a fossil endocast. Alice M. Clement, Robin Strand, Johan Nysjö, John A. Long, and Per E. Ahlberg. In Royal Society Open Science, volume 3, number 7, 2016. (DOI, Fulltext).
14. Estimation of Feret's diameter from pixel coverage representation of a shape. Slobodan Drazic, Natasa Sladoje, and Joakim Lindblad. In Pattern Recognition Letters, volume 80, pp 37-45, 2016. (DOI).
15. Analysis of the distribution of CD103 on CD8 T cells in blood and genital mucosa of HIV-infected female sex workers. Anna Gibbs, Marcus Buggert, Petter Ranefall, Andrea Introini, Stanley Cheuk, Liv Eidsmo, Taha Hirbod, Terry B. Ball, Joshua Kimani, Rupert Kaul, Annika C. Karlsson, Carolina Wählby, Kristina Broliden, and Annelie Tjernlund. In AIDS Research and Human Retroviruses, volume 32, number S1, pp 307-307, 2016.
16. Precision automation of cell type classification and sub-cellular fluorescence quantification from laser scanning confocal images. Hardy C. Hall, Azadeh Fakhrzadeh, Cris L. Luengo Hendriks, and Urs Fischer. In Frontiers in Plant Science, volume 7, 2016. (DOI, Fulltext).
17. A segmentation-free handwritten word spotting approach by relaxed feature matching. Anders Hast and Alicia Fornés. In Proc. 12th IAPR Workshop on Document Analysis Systems, pp 150-155, IEEE, 2016. (DOI).
18. The Challenges and Advantages with a Parallel Implementation of Feature Matching. Anders Hast and Andrea Marchetti. In Proc. 11th International Conference on Computer Vision Theory and Applications, 2016.
19. Signature of a Shape Based on Its Pixel Coverage Representation. Vladimir Ilic, Joakim Lindblad, and Nataša Sladoje. In Discrete Geometry for Computer Imagery, DGCI 2016. Lecture Notes in Computer Science, Vol. 9647, pp. 181-193, Springer 2016: 19th IAPR International Conference, DGCI 2016, Nantes, France, April 18-20, 2016. Proceedings, pp 181-193, Springer Berlin/Heidelberg, 2016. (DOI).
20. Image Analysis and Deep Learning for Applications in Microscopy. Omer Ishaq. Ph.D. thesis, Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology nr 1371, Acta Universitatis Upsaliensis, Uppsala, 2016. (fulltext, preview image).
21. Fourth generation of next-generation sequencing technologies: Promise and consequences. Rongqin Ke, Marco Mignardi, Thomas Hauling, and Mats Nilsson. In Human Mutation, volume 37, number 12, pp 1363-1367, 2016. (DOI, Fulltext).
22. Feature augmented deep neural networks for segmentation of cells. Sajith Kecheril Sadanandan, Petter Ranefall, and Carolina Wählby. In Computer Vision – ECCV 2016 Workshops: Part I, volume 9913 of Lecture Notes in Computer Science, pp 231-243, Springer, 2016. (DOI).
23. Segmentation and track-analysis in time-lapse imaging of bacteria. Sajith Kecheril Sadanandan, Özden Baltekin, Klas E. G. Magnusson, Alexis Boucharin, Petter Ranefall, Joakim Jaldén, Johan Elf, and Carolina Wählby. In IEEE Journal on Selected Topics in Signal Processing, volume 10, number 1, pp 174-184, 2016. (DOI).
24. On the influence of interpolation method on rotation invariance in texture recognition. Gustaf Kylberg and Ida-Maria Sintorn. In EURASIP Journal on Image and Video Processing, volume 2016, 2016. (DOI, Fulltext).
25. Fast vascular skeleton extraction algorithm. Kristína Lidayová, Hans Frimmel, Chunliang Wang, Ewert Bengtsson, and Örjan Smedby. In Pattern Recognition Letters, volume 76, pp 67-75, 2016. (DOI).
26. Visualisation and evaluation of flood uncertainties based on ensemble modelling. Nancy Joy Lim, S. Anders Brandt, and Stefan Seipel. In International Journal of Geographical Information Science, volume 30, number 2, pp 240-262, Taylor & Francis, 2016. (DOI).
27. Hand-held Augmented Reality for Facility Maintenance. Fei Liu. Ph.D. thesis, Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology nr 1412, Acta Universitatis Upsaliensis, Uppsala, 2016. (fulltext, preview image).
28. Estimating a structural bottle neck for eye–brain transfer of visual information from 3D-volumes of the optic nerve head from a commercial OCT device. Filip Malmberg, Camilla Sandberg-Melin, and Per G. Söderberg. In Ophthalmic Technologies XXVI, volume 9693 of Proc. SPIE, SPIE - International Society for Optical Engineering, Bellingham, WA, 2016. (DOI).
29. PopulationProfiler: A Tool for Population Analysis and Visualization of Image-Based Cell Screening Data. Damian J. Matuszewski, Carolina Wählby, Jordi Carreras-Puigvert, and Ida-Maria Sintorn. In PLOS ONE, volume 11, number 3, 2016. (DOI, Fulltext).
30. New technologies for DNA analysis: a review of the READNA Project. Steven McGinn, David Bauer, Thomas Brefort, Liqin Dong, Afaf El-Sagheer, Abdou Elsharawy, Geraint Evans, Elin Falk-Sörqvist, Michael Forster, Simon Fredriksson, Peter Freeman, Camilla Freitag, Joachim Fritzsche, Spencer Gibson, Mats Gullberg, Marta Gut, Simon Heath, Isabelle Heath-Brun, Andrew J. Heron, Johannes Hohlbein, Rongqin Ke, Owen Lancaster, Ludovic Le Reste, Giovanni Maglia, Rodolphe Marie, Florence Mauger, Florian Mertes, Marco Mignardi, Lotte Moens, Jelle Oostmeijer, Ruud Out, Jonas Nyvold Pedersen, Fredrik Persson, Vincent Picaud, Dvir Rotem, Nadine Schracke, Jennifer Sengenes, Peer F. Stähler, Björn Stade, David Stoddart, Xia Teng, Colin D. Veal, Nathalie Zahra, Hagan Bayley, Markus Beier, Tom Brown, Cees Dekker, Björn Ekström, Henrik Flyvbjerg, Andre Franke, Simone Guenther, Achillefs N. Kapanidis, Jane Kaye, Anders Kristensen, Hans Lehrach, Jonathan Mangion, Sascha Sauer, Emile Schyns, Jörg Tost, Joop M. L. M. van Helvoort, Pieter J. van der Zaag, Jonas O. Tegenfeldt, Anthony J. Brookes, Kalim Mir, Mats Nilsson, James P. Willcocks, and Ivo G. Gut. In New Biotechnology, volume 33, number 3, pp 311-330, 2016. (DOI).
31. Signed Distance Fields for Modeling Surgical Guides and Plates from CT Images. Fredrik Nysjö, Pontus Olsson, Filip Malmberg, Ingrid B. Carlbom, and Ingela Nyström. In Proc, Swedish Symposium on Image Analysis: SSBA 2016, 2016.
32. Interactive 3D Image Analysis for Cranio-Maxillofacial Surgery Planning and Orthopedic Applications. Johan Nysjö. Ph.D. thesis, Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology nr 1411, Acta Universitatis Upsaliensis, Uppsala, 2016. (fulltext, preview image).
33. Comparison of walking and traveling-wave piezoelectric motors as actuators in kinesthetic haptic devices. Pontus Olsson, Fredrik Nysjö, Ingrid B. Carlbom, and Stefan Johansson. In IEEE Transactions on Haptics, volume 9, number 3, pp 427-431, 2016. (DOI, Fulltext).
34. Automatic grading of breast cancer from whole slide images of Ki67 stained tissue sections. Petter Ranefall, Carolina Wählby, and Ewert Bengtsson. In , 2016.
35. Fast Adaptive Local Thresholding Based on Ellipse fit. Petter Ranefall, Sajith Kecheril Sadanandan, and Carolina Wählby. In , Scripta minora Bibliothecae regiae Universitatis UpsaliensisIEEE International Symposium on Biomedical Imaging, 2016. (Fulltext).
36. Global And Local Adaptive Gray-level Thresholding Based on Object Features. Petter Ranefall, Sajith Kecheril Sadanandan, and Carolina Wählby. In Swedish Symposium on Image Analysis 2016, 2016.
37. Global Gray-level Thresholding Based on Object Size. Petter Ranefall and Carolina Wählby. In Cytometry Part A, volume 89A, number 4, pp 385-390, John Wiley & Sons, 2016. (DOI).
38. A survey on skeletonization algorithms and their applications. Punam K. Saha, Gunilla Borgefors, and Gabriella Sanniti di Baja. In Pattern Recognition Letters, volume 76, pp 3-12, 2016. (DOI).
39. Fuzzy Segmentation of Synthetic and MRI Volume Data sampled on Optimal Lattices. Elisabeth Schold Linnér, Joel Kullberg, and Robin Strand. In , 2016. Publication status: Submitted
40. LatticeLibrary and BccFccRaycaster: Software for processing and viewing 3D data on optimal sampling lattices. Elisabeth Schold Linnér, Max Morén, Karl-Oskar Smed, Johan Nysjö, and Robin Strand. In SoftwareX, volume 5, pp 16-24, 2016. (DOI, Fulltext).
41. 3D game technology in property formation. Stefan Seipel, Goran Milutinovic, and Martin Andrée. In Proc. 16th International Multidisciplinary Scientific GeoConference, International Multidisciplinary Scientific GeoConference-SGEM, pp 539-546, 2016. (DOI).
42. Minimal paths by sum of distance transforms. Robin Strand. In Discrete Geometry for Computer Imagery, volume 9647 of Lecture Notes in Computer Science, pp 349-358, Springer, 2016. (DOI).
43. Automated detection of cilia in low magnification transmission electron microscopy images using template matching. Amit Suveer, Nataša Sladoje, Joakim Lindblad, Anca Dragomir, and Ida-Maria Sintorn. In Biomedical Imaging (ISBI), 2016 IEEE 13th International Symposium on, IEEE International Symposium on Biomedical Imaging, pp 386-390, IEEE, 2016. (DOI, Fulltext).
44. Analysis of the variation in OCT measurements of a structural bottle neck for eye–brain transfer of visual information from 3D-volumes of the optic nerve head, PIMD-Average [0;2?]. Per G. Söderberg, Filip Malmberg, and Camilla Sandberg-Melin. In Ophthalmic Technologies XXVI, volume 9693 of Proc. SPIE, SPIE - International Society for Optical Engineering, Bellingham, WA, 2016. (DOI).
45. Automatic quantification of fluorescence signal in rat lens epithelium. Nooshin Talebizadeh, Zhaohua Yu, Nanna Zhou Hagström, Carolina Wählby, and Per G. Söderberg. In Investigative Ophthalmology and Visual Science, volume 57, number 12, 2016.
46. Estimating manuscript production dates using both image and language data. Fredrik Wahlberg, Lasse Mårtensson, and Anders Brun. In Proceedings of SSBA, 2016, 2016.
47. Historical Manuscript Production Date Estimation using Deep Convolutional Neural Networks. Fredrik Wahlberg, Tomas Wilkinson, and Anders Brun. In , International Conference on Handwriting Recognition, pp 205-210, IEEE, 2016. (DOI, fulltext:postprint).
48. Large scale continuous dating of medieval scribes using a combined image and language model. Fredrik Wahlberg, Lasse Mårtensson, and Anders Brun. In , 2016. (DOI, fulltext:postprint).
49. Semantic and Verbatim Word Spotting using Deep Neural Networks. Tomas Wilkinson and Anders Brun. In Proceedings Of 2016 15Th International Conference On Frontiers In Handwriting Recognition (Icfhr), International Conference on Handwriting Recognition, pp 307-312, 2016. (DOI, fulltext:postprint).
50. Skin lamellar bodies are not discrete vesicles but part of a tubuloreticular network. Lianne den Hollander, HongMei Han, Matthijs de Winter, Lennart Svensson, Sergej Masich, Bertil Daneholt, and Lars Norlén. In Acta Dermato-Venereologica, volume 96, number 3, pp 303-309, 2016. (DOI, Fulltext).
51. Segmentation of shadows and water bodies in high resolution images using ancillary data. Julia Åhlén and Stefan Seipel. In Proc. 16th International Multidisciplinary Scientific GeoConference, International Multidisciplinary Scientific GeoConference-SGEM, pp 827-834, 2016. (DOI).

1. Calving events detection and quantification from time-lapse images in Tunabreen glacier. Sigit Adinugroho, Dorothée Vallot, Pontus Westrin, and Robin Strand. In Proc. 9th International Conference on Information &amp; Communication Technology and Systems, pp 61-65, IEEE, Piscataway, NJ, 2015. (DOI).
2. Comparing and visualizing titanium implant integration in rat bone using 2D and 3D techniques. Anna Arvidsson, Hamid Sarve, and Carina B. Johansson. In Journal of Biomedical Materials Research. Part B - Applied biomaterials, volume 103, number 1, pp 12-20, 2015. (DOI).
3. Blur detection and visualization in histological whole slide images. Christophe Avenel and Ingrid Carlbom. In Proc. 10th International Conference on Mass Data Analysis of Images and Signals, IBaI, Leipzig, Germany, 2015.
4. Topological clustering guided document binarization. Kalyan Ram Ayyalasomayajula and Anders Brun. Svenska Sällskapet för Automatiserad Bildanalys, 2015. (fulltext).
5. Compaction of rolling circle amplification products increases signal integrity and signal–to–noise ratio. Carl-Magnus Clausson, Linda Arngården, Omer Ishaq, Axel Klaesson, Malte Kühnemund, Karin Grannas, Björn Koos, Xiaoyan Qian, Petter Ranefall, Tomasz Krzywkowski, Hjalmar Brismar, Mats Nilsson, Carolina Wählby, and Ola Söderberg. In Scientific Reports, volume 5, pp 12317:1-10, 2015. (DOI, Fulltext).
6. Brain – Endocast relationship in the Australian lungfish, <em>Neoceratodus forsteri</em>, elucidated from tomographic data (Sarcopterygii: Dipnoi). Alice M. Clement, Johan Nysjö, Robin Strand, and Per E. Ahlberg. In PLOS ONE, volume 10, number 10, 2015. (DOI, Fulltext).
7. Adaptive hit or miss transform. Vladimir Curic, Sébastien Lefèvre, and Cris L. Luengo Hendriks. In Mathematical Morphology and Its Applications to Signal and Image Processing, volume 9082 of Lecture Notes in Computer Science, pp 741-752, Springer, 2015. (DOI).
8. Computer Assisted Pap Smear Analyser for Cervical Cancer Screening using Quantitative Microscopy. Rajasekharan Usha Deepak, Ramakrishnan Rajesh Kumar, Neendoorthalackal Balakrishnan Byju, Pundluvalu Nataraju Sharathkumar, Chandran Pournami, Salam Sibi, Ewert Bengtsson, and Kunjuraman Sujathan. In Journal of Cytology & Histology, volume 6, number S3, 2015. (DOI, Fulltext).
9. ?LBP – a novel member of the Local Binary Pattern family based on ?-cutting. Marija Delic, Joakim Lindblad, and Natasa Sladoje. In Proc. 9th International Symposium on Image and Signal Processing and Analysis, pp 13-18, IEEE, 2015. (DOI).
10. Recreating with photogrammetric techniques a submerged megalithic landscape: the case of the salas reservoir. B. Estevez, M. Pazos, J. M. Franco, and Anders Hast. In 3 Encontro Internacional de Arqueoloxia de Vilalba, pp 9-16, 2015.
11. Computerized Cell and Tissue Analysis. Azadeh Fakhrzadeh. Ph.D. thesis, Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology nr 1262, Acta Universitatis Upsaliensis, Uppsala, 2015. (fulltext, preview image).
12. Acrosome integrity assessment of boar spermatozoa images using an early fusion of texture and contour descriptors. Oscar García-Olalla, Enrique Alegre, Laura Fernández-Robles, Patrik Malm, and Ewert Bengtsson. In Computer Methods and Programs in Biomedicine, volume 120, number 1, pp 49-64, 2015. (DOI).
13. A Simple and Efficient Feature Descriptor for Fast Matching. Anders Hast, Victoria Sablina, Gustav Kylberg, and Ida-Maria Sintorn. In WSCG, pp 135-142, 2015.
14. Clustering in 2D as a Fast Deterministic Alternative to RANSAC. Anders Hast and Gustav Kylberg. In , 2015.
15. Interest Point Detection Based on the Extended Structure Tensor with a Scale Space Parameter. Anders Hast. In International Conference on Computer Vision Theory and Applications, pp 1-8, 2015.
16. Stereo Visualisation of Historical Aerial Photos as a Valuable Tool for Archeological Research. Anders Hast and Andrea Marchetti. In Computer Applications and Quantitative Methods in Archaeology, CAA, pp 1-3, 2015.
17. Stereo Visualisation of Historical Aerial Photos – a Valuable Digital Heritage Research Tool. Anders Hast and Andrea Marchetti. In 2015 Digital Heritage International Congress, Vol 2: Analysis &amp; Interpretation Theory, Methodologies, Preservation &amp; Standards Digital Heritage Projects &amp; Applications, pp 663-666, 2015.
18. Precise Euclidean distance transforms in 3D from voxel coverage representation. Vladimir Ilic, Joakim Lindblad, and Natasa Sladoje. In Pattern Recognition Letters, volume 65, pp 184-191, 2015. (DOI).
19. Next-Generation Pathology: Surveillance of Tumor Microecology. Björn Koos, Masood Kamali-Moghaddam, Leonor David, Manuel Sobrinho-Simoes, Anna Dimberg, Mats Nilsson, Carolina Wählby, and Ola Söderberg. In Journal of Molecular Biology, volume 427, number 11, pp 2013-2022, 2015. (DOI, Fulltext).
20. A histopathological tool for quantification of biomarkers with sub-cellular resolution. Andreas Kårsnäs, Robin Strand, Johan Doré, Thomas Ebstrup, Michael Lippert, and Kim Bjerrum. In Computer Methods in Biomechanics and Biomedical Engineering: Imaging & Visualization, volume 3, number 1, pp 25-46, 2015. (DOI).
21. Multimodal histological image registration using locally rigid transforms. Andreas Kårsnäs and Robin Strand. In Proc. Interactive Medical Image Computing Workshop, 2015.
22. Coverage segmentation of 3D thin structures. Kristína Lidayová, Joakim Lindblad, Nataša Sladoje, Hans Frimmel, Chunliang Wang, and Örjan Smedby. In Proc. 5th International Conference on Image Processing Theory, Tools and Applications, pp 23-28, IEEE, Piscataway, NJ, 2015. (DOI).
23. Exact linear time Euclidean distance transforms of grid line sampled shapes. Joakim Lindblad and Natasa Sladoje. In Mathematical Morphology and its Applications to Signal and Image Processing, volume 9082 of Lecture Notes in Computer Science, pp 645-656, Springer, 2015. (DOI).
24. High-resolution reconstruction by feature distance minimization from multiple views of an object. Joakim Lindblad, Natasa Sladoje, Amit Suveer, Anca Dragomir, and Ida-Maria Sintorn. In Proc. 5th International Conference on Image Processing Theory, Tools and Applications, pp 29-34, IEEE, Piscataway, NJ, 2015. (DOI).
25. Microscopy image enhancement for cost-effective cervical cancer screening. Joakim Lindblad, Ewert Bengtsson, and Nataša Sladoje. In Image Analysis, volume 9127 of Lecture Notes in Computer Science, pp 440-451, Springer, 2015. (DOI).
26. Infrared-visible image registration for augmented reality-based thermographic building diagnostics. Fei Liu and Stefan Seipel. In Visualization in Engineering, volume 3, pp 16:1-15, Springer, 2015. (DOI, Fulltext).
27. Magnetic resonance imaging cooling–reheating protocol indicates decreased fat fraction via lipid consumption in suspected brown adipose tissue. Elin Lundström, Robin Strand, Lars Johansson, Peter Bergsten, Håkan Ahlström, and Joel Kullberg. In PLOS ONE, volume 10, number 4, 2015. (DOI, Fulltext).
28. Automatic 3DS Conversion of Historical Aerial Photographs. Francesco Malapelle, Anders Hast, Andrea Fusiello, B. Rossi, P. Fragneto, and Andrea Marchetti. In IC3D 2015, International Conference on 3D Imaging, 2015.
29. Simulation of bright-field microscopy images depicting pap-smear specimen. Patrik Malm, Anders Brun, and Ewert Bengtsson. In Cytometry Part A, volume 87, number 3, pp 212-226, 2015. (DOI, fulltext:print).
30. Interactive Deformation of Volume Images for Image Registration. Filip Malmberg, Robin Strand, and Joel Kullberg. In Proc. Interactive Medical Image Computing Workshop, 2015. (External link).
31. Intracranial volume normalization methods: Considerations when investigating gender differences in regional brain volume. Richard Nordenskjöld, Filip Malmberg, Elna-Marie Larsson, Andrew Simmons, Håkan Ahlström, Lars Johansson, and Joel Kullberg. In Psychiatry Research, volume 231, number 3, pp 227-235, 2015. (DOI).
32. BoneSplit - A 3D Texture Painting Tool for Interactive Bone Separation in CT Images. Johan Nysjö, Filip Malmberg, Ida-Maria Sintorn, and Ingela Nyström. In Journal of WSCG, volume 23, number 2, pp 157-166, 2015.
33. Teaching OpenGL and Computer Graphics with Programmable Shaders. Johan Nysjö and Anders Hast. In SIGRAD, pp 1-3, 2015.
34. Haptics with Applications to Cranio-Maxillofacial Surgery Planning. Pontus Olsson. Ph.D. thesis, Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology nr 1289, Acta Universitatis Upsaliensis, Uppsala, 2015. (fulltext, preview image).
35. Haptics-assisted Virtual Planning of Bone, Soft Tissue, and Vessels in Fibula Osteocutaneous Free Flaps. Pontus Olsson, Fredrik Nysjö, Andrés Rodríguez-Lorenzo, Andreas Thor, Jan-Michaél Hirsch, and Ingrid B. Carlbom. In Plastic and Reconstructive Surgery - Global Open, volume 3, number 8, Wolters Kluwer, 2015. (DOI).
36. Visuohaptic bone saw simulator: Combining vibrotactile and kinesthetic feedback. Pontus Olsson, Fredrik Nysjö, Neeru Singh, Andreas Thor, and Ingrid Carlbom. In Proc. 8th ACM SIGGRAPH Asia Technical Briefs, pp 10:1-4, ACM Press, New York, 2015. (DOI).
37. Triangulation Painting. Max Pihlström, Anders Hast, and Anders Brun. In SIGRAD, pp 1-4, 2015.
38. Your New Default  Thresholding Method?: A robust global gray-level thresholding method based on object features. Petter Ranefall and Carolina Wählby. In BioImage Informatics Conference 2015, 2015.
39. Digital topology and geometry in medical image processing: A survey. Punam K. Saha, Robin Strand, and Gunilla Borgefors. In IEEE Transactions on Medical Imaging, volume 34, number 9, pp 1940-1964, 2015. (DOI).
40. Image processing on optimal volume sampling lattices: Thinking outside the boxBildbehandling på optimala samplingsgitter: Att tänka utanför ramen. Elisabeth Schold Linnér. Ph.D. thesis, Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology nr 1314, Acta Universitatis Upsaliensis, Uppsala, 2015. (fulltext, preview image).
41. Fast evaluation of the robust stochastic watershed. Bettina Selig, Filip Malmberg, and Cris L. Luengo Hendriks. In Mathematical Morphology and Its Applications to Signal and Image Processing, volume 9082 of Lecture Notes in Computer Science, pp 705-716, Springer, 2015. (DOI).
42. Fully automatic evaluation of the corneal endothelium from in vivo confocal microscopy. Bettina Selig, Koenraad A. Vermeer, Bernd Rieger, Toine Hillenaar, and Cris L. Luengo Hendriks. In BMC Medical Imaging, volume 15, 2015. (DOI, Fulltext).
43. Automated Image Acquisition and Particle Size Distribution in the MiniTEM Instrument. Ida-Maria Sintorn, Gustaf Kylberg, Lars Haag, and Rickard Nordström. In , 2015.
44. Effect of pre-fixation delay and freezing on mink testicular endpoints for environmental research. Ellinor Spörndly-Nees, Elisabeth Ekstedt, Ulf Magnusson, Azadeh Fakhrzadeh, Cris L. Luengo Hendriks, and Lena Holm. In PLOS ONE, volume 10, number 5, 2015. (DOI, fulltext:print).
45. Asymmetric supercapacitors based on carbon nanofibre and polypyrrole/nanocellulose composite electrodes. Petter Tammela, Zhaohui Wang, Sara Frykstrand, Peng Zhang, Ida-Maria Sintorn, Leif Nyholm, and Maria Strömme. In RSC Advances, volume 5, number 21, pp 16405-16413, 2015. (DOI).
46. Estimation of linear deformations of 2D and 3D fuzzy objects. Attila Tanács, Joakim Lindblad, Nataša Sladoje, and Zoltan Kato. In Pattern Recognition, volume 48, number 4, pp 1391-1403, 2015. (DOI).
47. Large scale style based dating of medieval manuscripts. Fredrik Wahlberg, Lasse Mårtensson, and Anders Brun. In Proc. 3rd International Workshop on Historical Document Imaging and Processing, pp 107-114, ACM Press, New York, 2015. (DOI, fulltext:postprint).
48. Writer identification using the Quill-Curvature feature in old manuscripts. Fredrik Wahlberg, Anders Brun, and Lasse Mårtensson. In Proceedings of SSBA, 2015, 2015.
49. A novel word segmentation method based on object detection and deep learning. Tomas Wilkinson and Anders Brun. In Advances in Visual Computing: 11th International Symposium, ISVC 2015, Las Vegas, NV, USA, December 14-16, 2015, Proceedings, Part I, volume 9474 of Lecture Notes in Computer Science, pp 231-240, Springer, 2015. (DOI, fulltext:postprint).
50. Experiments on Large Scale Document Visualization using Image-based Word Clouds. Tomas Wilkinson and Anders Brun. Technical report / Department of Information Technology, Uppsala University nr 2015-022, 2015. (fulltext).
51. Visualizing document image collections using image-based word clouds. Tomas Wilkinson and Anders Brun. In Advances in Visual Computing: 11th International Symposium, ISVC 2015, Las Vegas, NV, USA, December 14-16, 2015, Proceedings, Part I, volume 9474 of Lecture Notes in Computer Science, pp 297-306, Springer, 2015. (DOI, fulltext:postprint).
52. Image Segmentation, Processing and Analysis in Microscopy and Life Science. Carolina Wählby. In Mathematical Models in Biology: Bringing Mathematics to Life, pp 1-16, Springer, 2015. (DOI).
53. Automatic Water Body Extraction From Remote Sensing Images Using Entropy. Julia Åhlén and Stefan Seipel. In SGEM2015 Conference Proceedings, International Multidisciplinary Scientific GeoConference-SGEM, pp 517-524, 2015. (DOI).

1. Distance Functions and Their Use in Adaptive Mathematical Morphology. Vladimir ?uri?. Ph.D. thesis, Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology nr 1137, Acta Universitatis Upsaliensis, Uppsala, 2014. (fulltext, preview image).
2. Automated Tissue Image Analysis Using Pattern Recognition. Jimmy Azar. Ph.D. thesis, Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology nr 1175, Acta Universitatis Upsaliensis, Uppsala, 2014. (fulltext, preview image).
3. Simple filter design for first and second order derivatives by a double filtering approach. Anders Hast. In Pattern Recognition Letters, volume 42, pp 65-71, Elsevier, 2014. (DOI).
4. An Evaluation of the Faster STORM Method for Super-resolution Microscopy. Omer Ishaq, Johan Elf, and Carolina Wählby. In Proceedings of the 22nd International Conference on Pattern Recognition, International Conference on Pattern Recognition, pp 4435-4440, 2014. (DOI).
5. Automatic Virus Identification using TEM: Image Segmentation and Texture AnalysisAutomatisk identifiering av virus med hjälp av transmissionselektronmikroskopi: bildsegmentering och texturanalys. Gustaf Kylberg. Ph.D. thesis, Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology nr 1122, Acta Universitatis Upsaliensis, Uppsala, 2014. (fulltext, preview image).
6. Image Analysis Methods and Tools for Digital Histopathology Applications Relevant to Breast Cancer Diagnosis. Andreas Kårsnäs. Ph.D. thesis, Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology nr 1128, Acta Universitatis Upsaliensis, Uppsala, 2014. (fulltext, preview image).
7. Multimodal histological image registration using locally rigid transforms. Andreas Kårsnäs and Robin Strand. In IEEE Transactions on Biomedical Engineering, 2014. Publication status: Submitted
8. Geovisualization of Uncertainty in Simulated Flood Maps. Nancy Joy Lim and Stefan Seipel. In Proceedings of the IADIS conference in Computer Graphics, Visualization, Computer Vision and Image Processing (CGCVIP), pp 206-214, 2014.
9. Linear time distances between fuzzy sets with applications to pattern matching and classification. Joakim Lindblad and Natasa Sladoje. In IEEE Transactions on Image Processing, volume 23, number 1, pp 126-136, 2014. (DOI).
10. A Graph-Based Implementation of the Anti-Aliased Euclidean Distance Transform. Elisabeth Linnér and Robin Strand. In Proceedings 22nd International Conference on Pattern Recognition (ICPR), 2014, International Conference on Pattern Recognition, pp 1025-1030, 2014. (DOI).
11. Anti-Aliased Euclidean Distance Transform on 3D Sampling Lattices. Elisabeth Linnér and Robin Strand. In Discrete Geometry for Computer Imagery: 18th IAPR International Conference, DGCI 2014, Siena, Italy, September 10-12, 2014. Proceedings, volume 8668 of Lecture Notes in Computer Science, pp 88-98, 2014. (DOI).
12. Detection of Façade Regions in Street View Images from Split-and-Merge of Perspective Patches. Fei Liu and Stefan Seipel. In Journal of Image and Graphics, volume 2, number 1, pp 8-14, 2014. (External link).
13. An efficient algorithm for exact evaluation of stochastic watersheds. Filip Malmberg and Cris L. Luengo Hendriks. In Pattern Recognition Letters, volume 47, pp 80-84, 2014. (DOI).
14. Automatic Mapping of Standing Dead Trees after an Insect Outbreak Using the Window Independent Context Segmentation Method. Michael Nielsen, Marco Heurich, Bo Malmberg, and Anders Brun. In Journal of forestry, volume 112, number 6, pp 564-571, 2014. (DOI).
15. A Streaming Distance Transform Algorithm for Neighborhood-Sequence Distances. Nicolas Normand, Robin Strand, Evenou Pierre, and Aurore Arlicot. In Image Processing On Line, volume 4, pp 196-203, 2014. (DOI, External link).
16. Custom Mandibular Implant Design with Deformable Models and Haptics. Fredrik Nysjö, Pontus Olsson, Jan-Michaél Hirsch, and Ingrid B. Carlbom. In Proc. Computer Assisted Radiology and Surgery (CARS). Fukuoka, Japan, June 25-28, pp 246-247, Springer Berlin/Heidelberg, 2014. (DOI).
17. The Giga-pixel Challenge: Full Resolution Image Analysis – Without Losing the Big Picture: An open-source approach for multi-scale analysis and visualization of slide-scanner data. Petter Ranefall, Alexandra Pacureanu, Christophe Avenel, Anne E. Carpenter, and Carolina Wählby. In , 2014. (fulltext:postprint).
18. Solving Geospatial Tasks in 2D and 3D Visualizations of Maps. Stefan Seipel. In Information Visualisation: Techniques, Usability and Evaluation, pp 222-271, Cambridge Scholars Publishing, 2014.
19. Virus recognition based on local texture. Ida-Maria Sintorn and Gustaf Kylberg. In Proceedings 22nd International Conference on Pattern Recognition (ICPR), 2014, International Conference on Pattern Recognition, pp 3227-3232, 2014. (DOI).
20. The Minimum Barrier Distance - Stability to seed point position. Robin Strand, Filip Malmberg, Punam Saha, and Elisabeth Linnér. In Discrete Geometry for Computer Imagery, DGCI 2014, volume 8668 of Lecture Notes in Computer Science, pp 111-121, 2014. (DOI).
21. Feature space de-noising for text recognition. Fredrik Wahlberg and Anders Brun. In Proceedings of SSBA, 2014, 2014.
22. Scribal Attribution using a Novel 3-D Quill-Curvature Feature Histogram. Fredrik Wahlberg, Lasse Mårtensson, and Anders Brun. In Proceedings International Conference on Frontiers in Handwriting Recognition (ICFHR), 2014, 2014. (fulltext:postprint).
23. Evaluation of the Automatic methods for Building Extraction. Julia Åhlén, Stefan Seipel, and Fei Liu. In International Journal of Computers and Communications, volume 8, pp 171-176, 2014.
24. Knowledge Based Single Building Extraction and Recognition. Julia Åhlén and Stefan Seipel. In Proceedings WSEAS International Conference on Computer Engineering and Applications, 2014, pp 29-35, 2014. (External link).
25. TIME-SPACE VISUALISATION OF AMUR RIVER CHANNEL CHANGES DUE TO FLOODING DISASTER. Julia Åhlén and Stefan Seipel. In Proceedings of International Multidisciplinary Scientific GeoScience Conference (SGEM), 2014, 2014. (DOI, External link).

1. Geomemories - A Platform for Visualizing Historical, Environmental and Geospatial Changes of the Italian Landscape. Matteo Abrate, Clara Bacciu, Anders Hast, Andrea Marchetti, Salvatore Minutoli, and Maurizio Tesconi. In ISPRS International Journal of Geo-Information. Special issue: Geospatial Monitoring and Modelling of Environmental Change, volume 2, number 2, pp 432-455, MDPI - Open Access Publishing, 2013. (DOI, Fulltext).
2. A Weight Sequence Distance Function. Nagy Benedek, Robin Strand, and Nicolas Normand. In : Mathematical Morphology and Its Applications to Signal and Image Processing, volume 7883 of Lecture Notes in Computer Science, pp 292-301, Springer Berlin/Heidelberg, 2013. (DOI).
3. A new quantitative approach for estimating bone cell connections from nano-CT images. Pei Dong, Alexandra Pacureanu, Maria Zuluaga, Cecile Olivier, Frederique Frouin, Quentin Grimal, and Francoise Peyrin. In Engineering in Medicine and Biology Society (EMBC), 2013 35th Annual International Conference of the IEEE, pp 3694-3697, IEEE, 2013. (DOI).
4. Blind Color Decomposition of Histological Images. Milan Gavrilovic, Jimmy Azar, Joakim Lindblad, Carolina Wählby, Ewert Bengtsson, Christer Busch, and Ingrid Carlbom. In IEEE Transactions on Medical Imaging, volume 32, number 6, pp 983-994, 2013. (DOI).
5. Optimal RANSAC - Towards a Repeatable Algorithm for Finding the Optimal Set. Anders Hast and Johan Nysjö. In Journal of WSCG, volume 21, number 1, pp 21-30, 2013.
6. Rotation Invariant Feature Matching - Based on Gaussian Filtered Log Polar Transform and Phase Correlation.. Anders Hast and Andrea Marchetti. In 8th International Symposium on Image and Signal Processing and Analysis: (ISPA 2013), pp 1-6, 2013.
7. Analysis of nuclei textures of fine needle aspirated cytology images for breast cancer diagnosis using complex Daubechies wavelets. Swamidoss Issac Niwas, P. Palanisamy, K. Sujathan, and Ewert Bengtsson. In Signal Processing, volume 93, number 10, pp 2828-2837, 2013. (DOI).
8. Automated classification of immunostaining patterns in breast tissue from the Human Protein Atlas. Swamidoss Issac Niwas, Andreas Kårsnäs, Virginie Uhlmann, Palanisamy Ponnusamy, Caroline Kampf, Martin Simonsson, Carolina Wählby, and Robin Strand. In Journal of Pathology Informatics, volume 4, number 14, 2013. (DOI, External link).
9. Color deconvolution method for breast tissue core biopsy images cell nuclei detection and analysis using multiresolution techniques. Swamidoss Issac Niwas, P. Palanisamy, and Ewert Bengtsson. In International Journal of Imaging and Robotics, volume 9, number 1, pp 61-72, 2013.
10. Coverage segmentation of thin structures by linear unmixing and local centre of gravity attraction. Kristína Lidayová, Joakim Lindblad, Nataša Sladoje, and Hans Frimmel. In Proc. 8th International Symposium on Image and Signal Processing and Analysis, pp 83-88, IEEE Signal Processing Society, 2013. (DOI).
11. Image Analysis in Support of Computer-Assisted Cervical Cancer Screening. Patrik Malm. Ph.D. thesis, Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology nr 1106, Acta Universitatis Upsaliensis, Uppsala, 2013. (fulltext, preview image).
12. Faster Fuzzy Connectedness via Precomputation. Filip Malmberg and Robin Strand. In Mathematical Morphology and Its Applications to Signal and Image Processing, volume 7883 of Lecture Notes in Computer Science, pp 476-483, Springer, 2013.
13. Precise 3D Angle Measurements in CT Wrist Images. Johan Nysjö, Albert Christersson, Ida-Maria Sintorn, Ingela Nyström, Sune Larsson, and Filip Malmberg. In Image Analysis and Processing – ICIAP 2013: Part II, volume 8157 of Lecture Notes in Computer Science, pp 479-488, Springer Berlin/Heidelberg, 2013. (DOI).
14. Evaluating 2D and 3D geovisualisations for basic spatial assessment. Stefan Seipel. In Behavior and Information Technology, volume 32, number 8, pp 845-858, 2013. (DOI).
15. Factors influencing high quality low voltage TEM imaging of biological routinely stained specimen. Ida-Maria Sintorn, Rickard Nordström, Lars Haag, Eva Coufalova, and Michal Drsticka. In Proceedings, part I, pp 321-322, 2013.
16. Towards automated Virus Detection and Identification using TEM. Ida-Maria Sintorn, Gustaf Kylberg, Rickard Nordström, Lars Haag, Eva Coufalova, and Michal Drsticka. In Proceedings, Part II, pp 397-398, 2013.
17. Feature Weight Optimization and Pruning in Historical Text Recognition. Fredrik Wahlberg and Anders Brun. In Advances of Visual Computing: 9th International Symposium, ISVC 2013, Rethymnon, Crete, Greece, July 29-31, 2013. Proceedings, Part II, volume 8034 of Lecture Notes in Computer Science, pp 98-107, Springer Berlin/Heidelberg, 2013. (DOI, fulltext:postprint).
18. Feature space denoising improves word spotting. Fredrik Wahlberg and Anders Brun. In Proc. 2nd International Workshop on Historical Document Imaging and Processing, pp 59-66, ACM Press, New York, 2013. (DOI, fulltext:postprint).

1. An image based high-throughput assay for chemical screening using zebrafish.. Omer Ishaq, Joseph Negri, Mark-Anthony Bray, Alexandra Pacureanu, and Carolina Wählby. In , 2012.
2. An Investigation on Nuclei of Histopathological Images using Curvelet Statistical Features. Swamidoss Issac Niwas, P. Palanisamy, and Ewert Bengtsson. SSBA'12, Symposium on Image Analysis, KTH-Stockholm, 2012.
3. Segmentation of virus particle candidates in transmission electron microscopy images. Gustaf Kylberg, Mats Uppström, Kjell-Olof Hedlund, Gunilla Borgefors, and Ida-Maria Sintorn. In Journal of Microscopy, volume 245, number 2, pp 140-147, Blackwell Publishing, 2012. (DOI).
4. Learning histopathological patterns. Andreas Kårsnäs, Anders L. Dahl, and Rasmus Larsen. In Journal of Pathology Informatics, volume 2, p 12, 2012. (DOI).
5. The Vectorial Minimum Barrier Distance. Andreas Kårsnäs, Robin Strand, and Punam K. Saha. In International Conference on Pattern Recognition, pp 792-795, 2012. (External link).
6. Comparison of Restoration Quality on Square and Hexagonal Grids using Normalized Convolution. Elisabeth Linner and Robin Strand. In Proceedings of the 21st International Conference on Pattern Recognition (ICPR), 2012.
7. Aliasing Properties of Voxels in Three-Dimensional Sampling Lattices. Elisabeth Linnér and Robin Strand. In Large Scale Scientific Computing, volume 7116 of Lecture Notes in Computer Science, pp 507-514, 2012. (DOI).
8. Seeded Segmentation Based on Object Homogeneity. Filip Malmberg, Robin Strand, Richard Nordenskjöld, and Joel Kullberg. In Proceedings of the 21st International Conference on Pattern Recognition (ICPR), pp 21-24, 2012. (External link, External link).
9. Smart Paint: A New Interactive Segmentation Method\\ Applied to MR Prostate Segmentation. Filip Malmberg, Robin Strand, Joel Kullberg, Richard Nordenskjöld, and Ewert Bengtsson. In Prostate MR Image Segmentation Grand Challenge (PROMISE'12), a MICCAI 2012 workshop, 2012. (External link).
10. 3D nano-CT: a new approach for imaging at cellular scale. Alexandra Pacureanu, Max Langer, Jean-Loïc Rose, Chantal Revol-Muller, and Francoise Peyrin. General Assembly of the French Society for Signal and Image Processing in Life Sciences (Invited talk), 2012.
11. Imaging of the Bone Cell Network with Nanoscale Synchrotron Radiation Computed Tomography. Alexandra Pacureanu, Max Langer, Chantal Revol-Muller, and Francoise Peyrin. SSBA Symposium, 2012.
12. Isotropic 3D imaging of biological specimens at micro and nano scale. Alexandra Pacureanu, Francoise Peyrin, Max Langer, Omer Ishaq, Amin Allalou, and Carolina Wählby. In , 2012.
13. Making isotropic 3D imaging at microscopic scale accessible to every lab. Alexandra Pacureanu, Omer Ishaq, Amin Allalou, and Carolina Wählby. BioImage Informatics, 2012.
14. Synchrotron radiation CT from the micro to nanoscale for the investigation of bone tissue. Francoise Peyrin, Pei Dong, Alexandra Pacureanu, Maria Zuluaga, Cecile Olivier, Max Langer, and Peter Cloetens. In Proceedings of SPIE: The International Society for Optical Engineering, volume 8506 of Proceedings of SPIE - The International Society for Optical Engineering, p 85060L, 2012. (DOI).
15. Optimization of semi-automated cell tracking using application-expert feed-back. Martin Simonsson, Ahmet Tugrul Bayrak, and Carolina Wählby. In , 2012.
16. Regional Zernike Moments for Texture Recognition. Ida-Maria Sintorn and Gustaf Kylberg. In Proceedings of the 21st International Conference on Pattern Recognition (ICPR), pp 1635-1638, 2012.
17. The coverage model and its use in image processing. Natasa Sladoje and Joakim Lindblad. In Selected Topics on Image Processing and Cryptology: Zbornik radova (Collection of Papers), volume 15(23) of Zbornik radova, pp 39-117, Mathematical Institute of the Serbian Academy of Sciences and Arts, Belgrade, Serbia, 2012. (External link).
18. Word Spotting in Pre-Modern Manuscripts using Dynamic Time Warping. Fredrik Wahlberg, Mats Dahllöf, Lasse Mårtensson, and Anders Brun. In Proceedings of SSBA, 2012, 2012.
19. An image analysis toolbox for high-throughput <em>C. elegans </em>assays. Carolina Wählby, Lee Kamentsky, Zihan H Liu, Tammy Riklin-Raviv, Annie L Conery, Eyleen O'Rourke, Katherine Sokolnicki, Orane Visvikis, Vebjorn Ljosa, Javier E Irazoqui, Polina Golland, Gary Ruvkun, Frederick M Ausubel, and Anne E Carpenter. In Nature Methods, volume 9, number 7, pp 714-716, 2012. (DOI).

1. Approaches for increasing throughput andinformation content of image-based zebrafishscreens. Amin Allalou, Vladimir Curic, Carlos Pardo-Martin, Mehmet Fatih Yanik, and Carolina Wählby. In Proceeding of SSBA 2011, 2011.
2. Methods for 2D and 3D Quantitative Microscopy of Biological Samples. Amin Allalou. Ph.D. thesis, Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology nr 856, Acta Universitatis Upsaliensis, Uppsala, 2011. (fulltext).
3. Distance measures between digital fuzzy objects and their applicability in image processing<em></em>. Vladimir Curic, Joakim Lindblad, and Natasa Sladoje. In Combinatorial Image Analysis, volume 6636 of Lecture Notes in Computer Science, pp 385-397, Springer Berlin/Heidelberg, 2011. (DOI).
4. Precise Estimation of the Projection of a Shape from a Pixel Coverage Representation. Slobodan Draži?, Joakim Lindblad, and Natasa Sladoje. In Proceedings of the 7th IEEE International Symposium on Image and Signal Processing and Analysis (ISPA), pp 569-574, IEEE Computer Society, 2011. (External link).
5. Spectral Image Processing with Applications in Biotechnology and Pathology. Milan Gavrilovic. Ph.D. thesis, Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology nr 876, Acta Universitatis Upsaliensis, Uppsala, 2011. (fulltext).
6. Tissue Separation for Quantitative Malignancy Grading of Prostate Cancer. Milan Gavrilovic, Azar Jimmy, Christer Busch, and Ingrid Carlbom. In Abstracts of Medicinteknikdagarna 2011, pp 32-32, 2011. (External link, External link).
7. Anti-aliased Euclidean distance transform. Stefan Gustavson and Robin Strand. In Pattern Recognition Letters, volume 32, number 2, pp 252-257, 2011. (DOI).
8. Kylberg Texture Dataset v. 1.0. Gustaf Kylberg. External report (Blue series) nr 35, Centre for Image Analysis, Swedish University of Agricultural Sciences and Uppsala University, Uppsala, 2011. (External link, fulltext).
9. Refinement of Segmented Virus Particel Candidates in TEM Images. Gustaf Kylberg and Ida-Maria Sintorn. SSBA'11, Symposium on Image Analysis, Linköping, 2011.
10. Virus texture analysis using local binary patterns and radial density profiles. Gustaf Kylberg, Mats Uppström, and Ida-Maria Sintorn. In Progress in Pattern Recognition, Image Analysis, Computer Vision, and Applications, volume 7042 of Lecture Notes in Computer Science, pp 573-580, Springer Berlin/Heidelberg, 2011. (DOI).
11. Regularized image denoising based on spectral gradient optimization. Tibor Lukic, Joakim Lindblad, and Natasa Sladoje. In Inverse Problems, volume 27, number 8, pp 085010:1-17, 2011. (DOI).
12. A Graph-based Framework for Sub-pixel Image Segmentation. Filip Malmberg, Joakim Lindblad, Natasa Sladoje, and Ingela Nyström. In Theoretical Computer Science, volume 412, number 15, pp 1338-1349, 2011. (DOI).
13. Generalized Hard Constraints for Graph Segmentation. Filip Malmberg, Robin Strand, and Ingela Nyström. In Image Analysis, 17th Scandinavian Conference. SCIA 2011., Lecture Notes in Computer Science, Springer, 2011.
14. Graph-based Methods for Interactive Image Segmentation. Filip Malmberg. Ph.D. thesis, Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology nr 813, Acta Universitatis Upsaliensis, Uppsala, 2011. (fulltext).
15. Image Foresting Transform: On-the-fly Computation of Segmentation Boundaries. Filip Malmberg. In Image Analysis: 17th Scandinavian Conference, SCIA 2011, Lecture notes in computer science, Springer, 2011.
16. Measurement of fibre–fibre contact in three-dimensional images of fibrous materials obtained from X-ray synchrotron microtomography. Filip Malmberg, Joakim Lindblad, Catherine Östlund, Karin Almgren, and E. Kristofer Gamstedt. In Nuclear Instruments and Methods in Physics Research Section A: Accelerators, Spectrometers, Detectors and Associated Equipment, volume 637, number 1, pp 143-148, 2011. (DOI).
17. Approximating Euclidean circles by neighbourhood sequences in a hexagonal grid. Benedek Nagy and Robin Strand. In Theoretical Computer Science, volume 412, number 15, pp 1364-1377, 2011. (DOI).
18. Image Filtering Methods for Biomedical Applications. M. Khalid Khan Niazi. Ph.D. thesis, Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology nr 852, Acta Universitatis Upsaliensis, Uppsala, 2011. (fulltext).
19. Path-Based Distance with Varying Weights andNeighborhood Sequences. Nicolas Normand, Robin Strand, Pierre Evenou, and Aurore Arlicot. In <em><em>Proceedings, International Conference on Discrete Geometry for Computer Imagery (DGCI 2011)</em></em>: <em></em>, volume 6607 of Lecture Notes in Computer Science, pp 199-210, Springer, Berlin Heidelberg, 2011. (DOI, External link).
20. Visualization and Haptics for Interactive Medical Image Analysis: Image Segmentation in Cranio-Maxillofacial Surgery Planning. Ingela Nyström, Johan Nysjö, and Filip Malmberg. In Visual Informatics: Sustaining Research and Innovations, volume 7066 of Lecture Notes in Computer Science, pp 1-12, Springer-Verlag, Berlin Heidelberg, 2011. (DOI, External link).
21. Whole Hand Haptics. Pontus Olsson, Ingrid Carlbom, Stefan Johansson, and Fredrik Nysjö. In Medicinteknikdagarna Oktober 11-12 2011, Linköping, Sweden, 2011.
22. Cuanto: A Tool for Quantification of Bone Tissue in the Proximityof Implants. Hamid Sarve, Amin Allalou, and Carina B. Johansson. In Proceedings of SSBA 2011, 2011.
23. A weighted neighbourhood sequence distance function with three local steps. Robin Strand and Benedek Nagy. In Proceedings of Image and Signal Processing and Analysis (ISPA), 2011 7th International Symposium on, IEEE Conference proceedings, pp 564-568, IEEE Computer Society, 2011. (External link).
24. Digital distance functions on three-dimensional grids. Robin Strand, Benedek Nagy, and Gunilla Borgefors. In Theoretical Computer Science, volume 412, number 15, pp 1350-1363, 2011. (DOI).
25. Sparse Object Representations by Digital Distance Functions. Robin Strand. In <em>Proceedings, International Conference on Discrete Geometry for Computer Imagery (DGCI 2011)</em>, volume 6607 of Lecture Notes in Computer Science, pp 211-222, Springer, Berlin Heidelberg, 2011. (DOI, External link).
26. Data Mining Medieval Documents by Word Spotting. Fredrik Wahlberg, Mats Dahllöf, Lasse Mårtensson, and Anders Brun. In Proceedings of the 2011 Workshop on Historical Document Imaging and Processing, pp 75-82, ACM, New York, 2011. (DOI, Full text, fulltext:postprint).
27. Indication of Methane Gas in IR-Imagery. Julia Åhlén and Stefan Seipel. In Proceedings of IADIS International Conference Computer Graphics, Visualization, Computer Vision and Image Processing 2011 (CGVCVIP 2011), pp 187-192, 2011.