Label-free deep learning-based species classification of bacteria imaged by phase-contrast microscopy

Hallström, Erik; Kandavalli, Vinodh; Ranefall, Petter; Elf, Johan et al.

Part of PloS Computational Biology, 2023

• DOI for Label-free deep learning-based species classification of bacteria imaged by phase-contrast microscopy
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3-D Attention-SEV-Net for Segmentation of Post-operative Glioblastoma with Interactive Correction of Over-Segmentation

Kundu, Swagata; Banerjee, Subhashis; Toumpanakis, Dimitrios; Wikström, Johan et al.

Part of Pattern Recognition and Machine Intelligence, PREMI 2023, p. 380-387, 2023

• DOI for 3-D Attention-SEV-Net for Segmentation of Post-operative Glioblastoma with Interactive Correction of Over-Segmentation

Age-Invariant Face Recognition using Face Feature Vectors and Embedded Prototype Subspace Classifiers

Hast, Anders

Part of Advanced Concepts for Intelligent Vision Systems, p. 88-99, 2023

• DOI for Age-Invariant Face Recognition using Face Feature Vectors and Embedded Prototype Subspace Classifiers

Guest Editorial Special Issue on Emerging Topics on Development and Learning

Luo, Dingsheng; Cangelosi, Angelo; Sciutti, Alessandra; Wan, Weiwei et al.

Part of IEEE Transactions on Cognitive and Developmental Systems, p. 1795-1800, 2023

• DOI for Guest Editorial Special Issue on Emerging Topics on Development and Learning

Consensus Ranking for Efficient Face Image Retrieval: A Novel Method for Maximising Precision and Recall

Hast, Anders

Part of Image Analysis and Processing – ICIAP 2023, p. 159-170, 2023

• DOI for Consensus Ranking for Efficient Face Image Retrieval: A Novel Method for Maximising Precision and Recall

Cell Segmentation of in situ Transcriptomics Data using Signed Graph Partitioning

Andersson, Axel; Behanova, Andrea; Wählby, Carolina; Malmberg, Filip

Part of Graph-Based Representations in Pattern Recognition, p. 139-148, 2023

• DOI for Cell Segmentation of in situ Transcriptomics Data using Signed Graph Partitioning

RegiSTORM: channel registration for multi-color stochastic optical reconstruction microscopy

ovrebo, Oystein; Ojansivu, Miina; Kartasalo, Kimmo; Barriga, Hanna M. G. et al.

Part of BMC Bioinformatics, 2023

• DOI for RegiSTORM: channel registration for multi-color stochastic optical reconstruction microscopy
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Generative appearance replay for continual unsupervised domain adaptation

Chen, Boqi; Thandiackal, Kevin; Pati, Pushpak; Göksel, Orcun

Part of Medical Image Analysis, p. 102924-102924, 2023

• DOI for Generative appearance replay for continual unsupervised domain adaptation
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Communicating Awareness: Designing a Framework for Cognitive Human-Agent Interaction for Autonomous Vehicles

Tanevska, Ana; Ghosh, Arabinda; Winkle, Katie; Castellano, Ginevra et al.

2023

Refusion: Enabling Large-Size Realistic Image Restoration With Latent-Space Diffusion Models

Luo, Ziwei; Gustafsson, Fredrik K.; Zhao, Zheng; Sjölund, Jens et al.

Part of 2023 IEEE/CVF Conference on Computer Vision and Pattern Recognition Workshops (CVPRW), p. 1680-1691, 2023

• DOI for Refusion: Enabling Large-Size Realistic Image Restoration With Latent-Space Diffusion Models

Automated detection, segmentation and measurement of major vessels and the trachea in CT pulmonary angiography

Kahraman, Ali T.; Fröding, Tomas; Toumpanakis, Dimitrios; Sladoje, Nataša et al.

Part of Scientific Reports, 2023

• DOI for Automated detection, segmentation and measurement of major vessels and the trachea in CT pulmonary angiography
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Sex Classification of Face Images using Embedded Prototype Subspace Classifiers.

Hast, Anders

Part of Proceedings of the 31th International Conference in Central Europe on Computer Graphics, Visualization and Computer Vision WSCG 2023, p. 43-52, 2023

Dental hygienists and dentists as providers of brush biopsies for oral mucosa screening

Edman, Kristina; Runow Stark, Christina; Basic, Vladimir; Lindblad, Joakim et al.

Part of International Journal of Dental Hygiene, p. 524-532, 2023

• DOI for Dental hygienists and dentists as providers of brush biopsies for oral mucosa screening
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Evaluating the utility of brightfield image data for mechanism of action prediction

Harrison, Philip John; Gupta, Ankit; Rietdijk, Jonne; Wieslander, Håkan et al.

Part of PloS Computational Biology, 2023

• DOI for Evaluating the utility of brightfield image data for mechanism of action prediction
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A whole-body diffusion MRI normal atlas: development, evaluation and initial use

Sjöholm, Therese; Tarai, Sambit; Malmberg, Filip; Strand, Robin et al.

Part of Cancer Imaging, 2023

• DOI for A whole-body diffusion MRI normal atlas: development, evaluation and initial use
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Weakly supervised joint whole-slide segmentation and classification in prostate cancer

Pati, Pushpak; Jaume, Guillaume; Ayadi, Zeineb; Thandiackal, Kevin et al.

Part of Medical Image Analysis, 2023

• DOI for Weakly supervised joint whole-slide segmentation and classification in prostate cancer

A Study of Augmentation Methods for Handwritten Stenography Recognition

Heil, Raphaela; Breznik, Eva

2023

• DOI for A Study of Augmentation Methods for Handwritten Stenography Recognition

Can Representation Learning for Multimodal Image Registration be Improved by Supervision of Intermediate Layers?

Wetzer, Elisabeth; Lindblad, Joakim; Sladoje, Nataša

Part of IbPRIA 2023: Pattern Recognition and Image Analysis, p. 261-275, 2023

• DOI for Can Representation Learning for Multimodal Image Registration be Improved by Supervision of Intermediate Layers?

Partial dimensional collapse in contrastive learning when using intermediate layers

Wetzer, Elisabeth; Lindblad, Joakim; Sladoje, Nataša

2023

Robust Imaging of Speed-of-Sound Using Virtual Source Transmission

Schweizer, Dieter; Rau, Richard; Bezek, Can Deniz; Kubik-Huch, Rahel A. et al.

Part of IEEE Transactions on Ultrasonics, Ferroelectrics and Frequency Control, p. 1-1, 2023

• DOI for Robust Imaging of Speed-of-Sound Using Virtual Source Transmission

Introducing Spatial Context in Patch-Based Deep Learning for Semantic Segmentation in Whole Body MRI

Breznik, Eva; Kullberg, Joel; Ahlström, Håkan; Strand, Robin

Part of Scandinavian Conference on Image Analysis, p. 214-228, 2023

Deep Active Learning for Glioblastoma Quantification

Banerjee, Subhashis; Strand, Robin

Part of Scandinavian Conference on Image Analysis, p. 190-200, 2023

Deep Curriculum Learning for Follow-up MRI Registration in Glioblastoma

Banerjee, Subhashis; Toumpanakis, Dimitrios; Dhara, Ashis; Wikström, Johan et al.

Part of Medical Imaging 2023, 2023

• DOI for Deep Curriculum Learning for Follow-up MRI Registration in Glioblastoma

Analytical Estimation of Beamforming Speed-of-Sound Using Transmission Geometry

Bezek, Can Deniz; Göksel, Orcun

Part of Ultrasonics, 2023

• DOI for Analytical Estimation of Beamforming Speed-of-Sound Using Transmission Geometry
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Lifelong Learning with Dynamic Convolutions for Glioma: Segmentation from Multi-Modal MRI

Banerjee, Subhashis; Strand, Robin

Part of Medical Imaging 2023, 2023

INSPIRE: Intensity and Spatial Information-Based Deformable Image Registration

Öfverstedt, Johan; Lindblad, Joakim; Sladoje, Nataša

Part of PLOS ONE, 2023

• DOI for INSPIRE: Intensity and Spatial Information-Based Deformable Image Registration
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Introducing spatial context in patch-based deep learning for semantic segmentation in whole body MRI

Breznik, Eva; Kullberg, Joel; Ahlström, Håkan; Strand, Robin

Part of Proceedings of the 22nd Scandinavian conference on image analysis (SCIA), 2023

Patient specific deep learning based segmentation for magnetic resonance guided prostate radiotherapy

Fransson, Samuel; Tilly, David; Strand, Robin

Part of Physics and Imaging in Radiation Oncology, p. 38-42, 2022

• DOI for Patient specific deep learning based segmentation for magnetic resonance guided prostate radiotherapy
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Re-Ranking Strategies in Cross-Modality Microscopy Retrieval

Wetzer, Elisabeth; Breznik, Eva; Lindblad, Joakim; Sladoje, Nataša

2022

MIMIR: Deep Regression for Automated Analysis of UK Biobank MRI Scans

Langner, Taro; Martínez Mora, Andrés; Strand, Robin; Ahlström, Håkan et al.

Part of Radiology: Artificial Intelligence, 2022

• DOI for MIMIR: Deep Regression for Automated Analysis of UK Biobank MRI Scans

Fast computation of mutual information in the frequency domain with applications to global multimodal image alignment

Öfverstedt, Johan; Lindblad, Joakim; Sladoje, Natasa

Part of Pattern Recognition Letters, p. 196-203, 2022

• DOI for Fast computation of mutual information in the frequency domain with applications to global multimodal image alignment
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Efficient Parallel Thinning of 3d Objects on the Body-centered Cubic Lattice

Brunner, David; Brunnett, Guido; Kronfeld, Thomas; Strand, Robin

Part of Computer-Aided Design, 2022

• DOI for Efficient Parallel Thinning of 3d Objects on the Body-centered Cubic Lattice

Serum levels of perfluoroalkyl substances (PFAS) and body composition - A cross-sectional study in a middle-aged population

Lind, P. Monica; Lind, Lars; Salihovic, Samira; Ahlström, Håkan et al.

Part of Environmental Research, p. 112677, 2022

• DOI for Serum levels of perfluoroalkyl substances (PFAS) and body composition - A cross-sectional study in a middle-aged population
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Probabilistic spatial analysis in quantitative microscopy with uncertainty-aware cell detection using deep Bayesian regression

Gomariz, Alvaro; Portenier, Tiziano; Nombela-Arrieta, Cesar; Göksel, Orcun

Part of Science Advances, 2022

• DOI for Probabilistic spatial analysis in quantitative microscopy with uncertainty-aware cell detection using deep Bayesian regression

Guest Editorial: Discrete Geometry and Mathematical Morphology

Malmberg, Filip; Lindblad, Joakim; Sladoje, Natasa

Part of Journal of Mathematical Imaging and Vision, p. 691-692, 2022

• DOI for Guest Editorial: Discrete Geometry and Mathematical Morphology

Improved geometric accuracy of whole body diffusion-weighted imaging at 1.5T and 3T using reverse polarity gradients

Sjöholm, Therese; Kullberg, Joel; Strand, Robin; Engström, M. et al.

Part of Scientific Reports, 2022

• DOI for Improved geometric accuracy of whole body diffusion-weighted imaging at 1.5T and 3T using reverse polarity gradients
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Cross-Sim-NGF: FFT-Based Global Rigid Multimodal Alignment of Image Volumes using Normalized Gradient Fields

Öfverstedt, Johan; Lindblad, Joakim; Sladoje, Natasa

2022

• DOI for Cross-Sim-NGF: FFT-Based Global Rigid Multimodal Alignment of Image Volumes using Normalized Gradient Fields

Rotation-Equivariant Semantic Instance Segmentation on Biomedical Images

Bengtsson Bernander, Karl; Lindblad, Joakim; Strand, Robin; Nystrom, Ingela

Part of MEDICAL IMAGE UNDERSTANDING AND ANALYSIS, MIUA 2022, p. 283-297, 2022

• DOI for Rotation-Equivariant Semantic Instance Segmentation on Biomedical Images

Haptic-Assisted Surgical Planning (HASP) in a Case of Bilateral Mandible Fracture

Moafi, Roya; Nysjö, Fredrik; Kämpe, Johan; Riben, Christopher et al.

Part of International Medical Case Reports Journal, p. 707-712, 2022

• DOI for Haptic-Assisted Surgical Planning (HASP) in a Case of Bilateral Mandible Fracture
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End-to-End Learning and Analysis of Infant Engagement During Guided Play: Prediction and Explainability

Fraile, Marc; Fawcett, Christine; Lindblad, Joakim; Sladoje, Nataša et al.

Part of ICMI '22, p. 444-454, 2022

• DOI for End-to-End Learning and Analysis of Infant Engagement During Guided Play: Prediction and Explainability
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Is image-to-image translation the panacea for multimodal image registration?: A comparative study

Lu, Jiahao; Öfverstedt, Johan; Lindblad, Joakim; Sladoje, Nataša

Part of PLOS ONE, 2022

• DOI for Is image-to-image translation the panacea for multimodal image registration?: A comparative study
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Towards Better Guided Attention and Human Knowledge Insertion in Deep Convolutional Neural Networks

Gupta, Ankit; Sintorn, Ida-Maria

2022

Is brightfield all you need for MoA prediction?

Gupta, Ankit; Harrison, Philip J; Wieslander, Håkan; Rietdijk, Jonne et al.

2022

SimSearch: A Human-in-The-Loop Learning Framework for Fast Detection of Regions of Interest in Microscopy Images

Gupta, Ankit; Sabirsh, Alan; Wählby, Carolina; Sintorn, Ida-Maria

Part of IEEE journal of biomedical and health informatics, p. 4079-4089, 2022

• DOI for SimSearch: A Human-in-The-Loop Learning Framework for Fast Detection of Regions of Interest in Microscopy Images
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End-to-end Multiple Instance Learning with Gradient Accumulation

Andersson, Axel; Koriakina, Nadezhda; Sladoje, Nataša; Lindblad, Joakim

Part of 2022 IEEE International Conference on Big Data (Big Data), p. 2742-2746, 2022

• DOI for End-to-end Multiple Instance Learning with Gradient Accumulation

Segmentation of Major Cerebral Vessel from MRA images and Evaluation using U-Net Family

Pal, Subhash; Banerjee, Subhashis; Toumpanakis, Dimitrios; Wikström, Johan et al.

Part of 2022 IEEE 6th International Conference on Condition Assessment Techniques in Electrical Systems (CATCON), p. 235-238, 2022

• DOI for Segmentation of Major Cerebral Vessel from MRA images and Evaluation using U-Net Family

Cross-Modality Sub-Image Retrieval using Contrastive Multimodal Image Representations

Breznik, Eva; Wetzer, Elisabeth; Lindblad, Joakim; Sladoje, Natasa

2022

• DOI for Cross-Modality Sub-Image Retrieval using Contrastive Multimodal Image Representations

Regular Use of Depot Medroxyprogesterone Acetate Causes Thinning of the Superficial Lining and Apical Distribution of Human Immunodeficiency Virus Target Cells in the Human Ectocervix

Edfeldt, Gabriella; Lajoie, Julie; Röhl, Maria; Oyugi, Julius et al.

Part of Journal of Infectious Diseases, p. 1151-1161, 2022

• DOI for Regular Use of Depot Medroxyprogesterone Acetate Causes Thinning of the Superficial Lining and Apical Distribution of Human Immunodeficiency Virus Target Cells in the Human Ectocervix
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Global Speed-of-Sound Prediction Using Transmission Geometry

Bezek, Can Deniz; Bilgin, Mert; Zhang, Lin; Göksel, Orcun

Part of Proceedings of the 2022 IEEE International Ultrasonics Symposium (IUS), p. 1-4, 2022

• DOI for Global Speed-of-Sound Prediction Using Transmission Geometry

Differentiable Zooming for Multiple Instance Learning on Whole-Slide Images

Thandiackal, Kevin; Chen, Boqi; Pati, Pushpak; Jaume, Guillaume et al.

Part of COMPUTER VISION, ECCV 2022, PT XXI, p. 699-715, 2022

• DOI for Differentiable Zooming for Multiple Instance Learning on Whole-Slide Images

A Hitchhiker's guide through the bio‐image analysis software universe

Haase, Robert; Fazeli, Elnaz; Legland, David; Doube, Michael et al.

Part of FEBS Letters, p. 2472-2485, 2022

• DOI for A Hitchhiker's guide through the bio‐image analysis software universe
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DCNN based Oral Cancer Screening using Whole Slide Cytology Images: Effect of Increased Patch Size

Chatterjee, Swarnadip; Sladoje, Nataša; Lindblad, Joakim

2022

A Spatially Detailed Approach to the Assessment of Rooftop Solar Energy Potential based on LiDAR Data

Aslani, Mohammad; Seipel, Stefan

Part of GISTAM, p. 56-63, 2022

• DOI for A Spatially Detailed Approach to the Assessment of Rooftop Solar Energy Potential based on LiDAR Data

Efficient Algorithms for Global Multimodal Image Registration

Öfverstedt, Johan; Lindblad, Joakim; Sladoje, Natasa

2022

Early Detection of Oral Potentially Malignant Disorders: A Review on Prospective Screening Methods with Regard to Global Challenges

Haj-Hosseini, Neda; Lindblad, Joakim; Hasséus, Bengt; Kumar, Vinay Vijaya et al.

Part of Journal of Maxillofacial and Oral Surgery, 2022

• DOI for Early Detection of Oral Potentially Malignant Disorders: A Review on Prospective Screening Methods with Regard to Global Challenges

AI based prostate analysis system trained without human supervision to predict patient outcome from tissue samples

Walhagen, Peter; Bengtsson, Ewert; Lennartz, Maximilian; Sauter, Guido et al.

Part of Journal of Pathology Informatics, 2022

• DOI for AI based prostate analysis system trained without human supervision to predict patient outcome from tissue samples

Rotationally Equivariant Representation Learning for Multimodal Images

Wetzer, Elisabeth; Pielawski, Nicolas; Öfverstedt, Johan; Lu, Jiahao et al.

2022

Label-Free Reverse Image Search of Multimodal Microscopy Images

Breznik, Eva; Wetzer, Elisabeth; Lindblad, Joakim; Sladoje, Natasa

2022

Restoration of Archival Images Using NeuralNetworks

Heil, Raphaela; Wahlberg, Fredrik

Part of Proceedings of the 6th Digital Humanities in the Nordic and Baltic Countries Conference (DHNB 2022), p. 79-93, 2022

Spectral Ultrasound Imaging of Speed-of-Sound and Attenuation Using an Acoustic Mirror

Chintada, Bhaskara Rao; Rau, Richard; Göksel, Orcun

Part of Frontiers in Physics, 2022

• DOI for Spectral Ultrasound Imaging of Speed-of-Sound and Attenuation Using an Acoustic Mirror
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Unsupervised Domain Adaptation with Contrastive Learning for OCT Segmentation

Gomariz, Alvaro; Lu, Huanxiang; Li, Yun Yvonna; Albrecht, Thomas et al.

Part of Medical Image Computing and Computer Assisted Intervention, MICCAI 2022, pt viii, p. 351-361, 2022

• DOI for Unsupervised Domain Adaptation with Contrastive Learning for OCT Segmentation

Hierarchical graph representations in digital pathology

Pati, Pushpak; Jaume, Guillaume; Foncubierta-Rodriguez, Antonio; Feroce, Florinda et al.

Part of Medical Image Analysis, 2022

• DOI for Hierarchical graph representations in digital pathology
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Computational analysis of subscapularis tears and pectoralis major transfers on muscular activity

Pean, Fabien; Favre, Philippe; Göksel, Orcun

Part of Clinical Biomechanics, 2022

• DOI for Computational analysis of subscapularis tears and pectoralis major transfers on muscular activity
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An image registration method for voxel-wise analysis of whole-body oncological PET-CT

Jönsson, Hanna; Ekström, Simon; Strand, Robin; Pedersen, Mette A et al.

Part of Scientific Reports, 2022

• DOI for An image registration method for voxel-wise analysis of whole-body oncological PET-CT
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Topology-Aware Learning for Volumetric Cerebrovascular Segmentation

Banerjee, Subhashis; Toumpanakis, Dimitrios; Dhara, Ashis Kumar; Wikström, Johan et al.

Part of 2022 IEEE International Symposium on Biomedical Imaging (IEEE ISBI 2022), p. 1-4, 2022

• DOI for Topology-Aware Learning for Volumetric Cerebrovascular Segmentation

Magnitude of Semicircle Tiles in Fourier-space: A Handcrafted Feature Descriptor for Word Recognition using Embedded Prototype Subspace Classifiers

Hast, Anders

Part of Journal of WSCG, p. 82-90, 2022

• DOI for Magnitude of Semicircle Tiles in Fourier-space: A Handcrafted Feature Descriptor for Word Recognition using Embedded Prototype Subspace Classifiers

TEM image restoration from fast image streams

Wieslander, Håkan; Wählby, Carolina; Sintorn, Ida-Maria

Part of PLOS ONE, 2021

• DOI for TEM image restoration from fast image streams
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Learning to see colours: Biologically relevant virtual staining for adipocyte cell images

Wieslander, Håkan; Gupta, Ankit; Bergman, Ebba; Hallström, Erik et al.

Part of PLOS ONE, 2021

• DOI for Learning to see colours: Biologically relevant virtual staining for adipocyte cell images
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Rapid development of cloud-native intelligent data pipelines for scientific data streams using the HASTE Toolkit

Blamey, Ben; Toor, Salman; Dahlö, Martin; Wieslander, Håkan et al.

Part of GigaScience, p. 1-14, 2021

• DOI for Rapid development of cloud-native intelligent data pipelines for scientific data streams using the HASTE Toolkit
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Towards automatic protein co-expression quantification in immunohistochemical TMA slides

Solorzano, Leslie; Pereira, Carla; Martins, Diana; Almeida, Raquel et al.

Part of IEEE journal of biomedical and health informatics, p. 393-402, 2021

• DOI for Towards automatic protein co-expression quantification in immunohistochemical TMA slides
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Phase-Aberration Correction in Shear-Wave Elastography Imaging Using Local Speed-of-Sound Adaptive Beamforming

Chintada, Bhaskara R.; Rau, Richard; Goksel, Orcun

Part of Frontiers in Physics, 2021

• DOI for Phase-Aberration Correction in Shear-Wave Elastography Imaging Using Local Speed-of-Sound Adaptive Beamforming
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Morphological Features Extracted by AI Associated with Spatial Transcriptomics in Prostate Cancer

Chelebian, Eduard; Avenel, Christophe; Kartasalo, Kimmo; Marklund, Maja et al.

Part of Cancers, 2021

• DOI for Morphological Features Extracted by AI Associated with Spatial Transcriptomics in Prostate Cancer
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Evaluation of in-house, haptic assisted surgical planning for virtual reduction of complex mandibular fractures

Nilsson, Johanna; Nysjö, Fredrik; Nyström, Ingela; Kämpe, Johan et al.

Part of International Journal of Computer Assisted Radiology and Surgery, p. 1059-1068, 2021

• DOI for Evaluation of in-house, haptic assisted surgical planning for virtual reduction of complex mandibular fractures
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Efficient and decision boundary aware instance selection for support vector machines

Aslani, Mohammad; Seipel, Stefan

Part of Information Sciences, p. 579-598, 2021

• DOI for Efficient and decision boundary aware instance selection for support vector machines
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Does visual saliency affect decision-making?

Milutinovic, Goran; Ahonen-Jonnarth, Ulla; Seipel, Stefan

Part of Journal of Visualization, p. 1267-1285, 2021

• DOI for Does visual saliency affect decision-making?
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Modality attention and sampling enables deep learning with heterogeneous marker combinations in fluorescence microscopy

Gomariz, Alvaro; Portenier, Tiziano; Helbling, Patrick M.; Isringhausen, Stephan et al.

Part of Nature Machine Intelligence, p. 799-811, 2021

• DOI for Modality attention and sampling enables deep learning with heterogeneous marker combinations in fluorescence microscopy

Graph-based image decoding for multiplexed in situ RNA detection

Partel, Gabriele; Wählby, Carolina

Part of 2020 25th International Conference on Pattern Recognition (ICPR), p. 3783-3790, 2021

• DOI for Graph-based image decoding for multiplexed in situ RNA detection
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Quantifying Explainers of Graph Neural Networks in Computational Pathology

Jaume, Guillaume; Pati, Pushpak; Bozorgtabar, Behzad; Foncubierta, Antonio et al.

Part of 2021 IEEE/CVF Conference on Computer Vision and Pattern Recognition, CVPR 2021, p. 8102-8112, 2021

• DOI for Quantifying Explainers of Graph Neural Networks in Computational Pathology

Time Of Arrival Delineation In Echo Traces For Reflection Ultrasound Tomography

Chintada, Bhaskara R; Rau, Richard; Göksel, Orcun

p. 1342-1345, 2021

• DOI for Time Of Arrival Delineation In Echo Traces For Reflection Ultrasound Tomography

Utilizing Uncertainty Estimation in Deep Learning Segmentation of Fluorescence Microscopy Images with Missing Markers

Gomariz, Alvaro; Egli, Raphael; Portenier, Tiziano; Nombela-Arrieta, Cesar et al.

2021

• DOI for Utilizing Uncertainty Estimation in Deep Learning Segmentation of Fluorescence Microscopy Images with Missing Markers

Replacing data augmentation with rotation-equivariant CNNs in image-based classification of oral cancer

Bengtsson Bernander, Karl; Lindblad, Joakim; Strand, Robin; Nyström, Ingela

2021

Learning Whole-Slide Segmentation from Inexact and Incomplete Labels Using Tissue Graphs

Anklin, Valentin; Pati, Pushpak; Jaume, Guillaume; Bozorgtabar, Behzad et al.

Part of Medical Image Computing and Computer Assisted Intervention, p. 636-646, 2021

• DOI for Learning Whole-Slide Segmentation from Inexact and Incomplete Labels Using Tissue Graphs

Strikethrough Removal from Handwritten Words Using CycleGANs

Heil, Raphaela; Vats, Ekta; Hast, Anders

Part of Document Analysis and Recognition -- ICDAR 2021, p. 572-586, 2021

• DOI for Strikethrough Removal from Handwritten Words Using CycleGANs

Word Recognition using Embedded Prototype Subspace Classifiers on a new Imbalanced Dataset

Hast, Anders; Vats, Ekta

Part of Journal of WSCG, p. 39-47, 2021

• DOI for Word Recognition using Embedded Prototype Subspace Classifiers on a new Imbalanced Dataset

Icke-invasiv kontroll av cellförändringar i munslemhinnan

Hirsch, Jan-Michaél; Haj-Hosseini, Neda; Krüger Weiner, Carina; Hasséus, Bengt et al.

Part of Tandläkartidningen, p. 48-55, 2021

Effects of distance transform choice in training with boundary loss

Breznik, Eva; Strand, Robin

2021

ImageJ and CellProfiler: Complements in Open‐Source Bioimage Analysis

Dobson, Ellen T.A.; Cimini, Beth; Klemm, Anna H; Wählby, Carolina et al.

Part of Current Protocols in Microbiology, 2021

• DOI for ImageJ and CellProfiler: Complements in Open‐Source Bioimage Analysis

Shorthand Secrets: Deciphering Astrid Lindgren's Stenographed Drafts with HTR Methods

Heil, Raphaela; Nauwerck, Malin; Hast, Anders

p. 169-177, 2021

The Effect of Within-Bag Sampling on End-to-End Multiple Instance Learning

Koriakina, Nadezhda; Sladoje, Natasa; Lindblad, Joakim

Part of Proceedings of the 12th International Symposium on Image and Signal Processing and Analysis (ISPA), p. 183-188, 2021

• DOI for The Effect of Within-Bag Sampling on End-to-End Multiple Instance Learning

Deep learning and conformal prediction for hierarchical analysis of large-scale whole-slide tissue images

Wieslander, Håkan; Harrison, Philip J.; Skogberg, Gabriel; Jackson, Sonya et al.

Part of IEEE journal of biomedical and health informatics, p. 371-380, 2021

• DOI for Deep learning and conformal prediction for hierarchical analysis of large-scale whole-slide tissue images
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CytoBrowser: a browser-based collaborative annotation platform for whole slide images

Rydell, Christopher; Lindblad, Joakim

Part of F1000 Research, 2021

• DOI for CytoBrowser: a browser-based collaborative annotation platform for whole slide images

Assessing Damage – Can the Crowd Interpret Colour and 3D Information?

Seffers, Gaëlle; Åhlén, Juia; Seipel, Stefan; Ooms, Kristien

Part of Cartographic Journal, p. 69-82, 2021

• DOI for Assessing Damage – Can the Crowd Interpret Colour and 3D Information?

Machine learning for cell classification and neighborhood analysis in glioma tissue

Solorzano, Leslie; Wik, Lina; Bontell, Thomas Olsson; Wang, Yuyu et al.

Part of Cytometry Part A, p. 1176-1186, 2021

• DOI for Machine learning for cell classification and neighborhood analysis in glioma tissue
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Content-Preserving Unpaired Translation from Simulated to Realistic Ultrasound Images

Tomar, Devavrat; Zhang, Lin; Portenier, Tiziano; Goksel, Orcun

Part of Medical Image Computing and Computer Assisted Intervention, p. 659-669, 2021

• DOI for Content-Preserving Unpaired Translation from Simulated to Realistic Ultrasound Images

Relationships Between Plasma Levels And Six Proinflammatory Interleukins And Body Composition Using A New Magnetic Resonance Imaging Voxel-based Technique

Strand, Robin; Kullberg, Joel; Ahlström, Håkan; Lind, Lars

Part of Cytokine: X, p. 100050, 2021

• DOI for Relationships Between Plasma Levels And Six Proinflammatory Interleukins And Body Composition Using A New Magnetic Resonance Imaging Voxel-based Technique

Contrastive Learning for Equivariant Multimodal Image Representations

Wetzer, Elisabeth; Pielawski, Nicolas; Breznik, Eva; Öfverstedt, Johan et al.

2021

Image-to-Image Translation in Multimodal Image Registration: How Well Does It Work?

Lu, Jiahao; Öfverstedt, Johan; Lindblad, Joakim; Sladoje, Natasa

2021

Estimating Mean Speed-of-Sound from Sequence-Dependent Geometric Disparities

Augustin, Xenia; Zhang, Lin; Goksel, Orcun

2021

Fast Computation of Mutual Information with Application to Global Multimodal Image Alignment of Micrographs

Öfverstedt, Johan; Lindblad, Joakim; Sladoje, Natasa

2021

Segmentation of Intracranial Aneurysm Remnant in MRA using Dual-Attention Atrous Net

Banerjee, Subhashis; Kumar Dhara, Ashis; Wikström, Johan; Strand, Robin

Part of 25th International Conference on Pattern Recognition (ICPR), p. 9265-9272, 2021

• DOI for Segmentation of Intracranial Aneurysm Remnant in MRA using Dual-Attention Atrous Net

Registration of Multimodal Microscopy Images using CoMIR – learned structural image representations

Wetzer, Elisabeth; Pielawski, Nicolas; Öfverstedt, Johan; Lu, Jiahao et al.

2021

Editorial of special section on CIARP 2019

Nyström, Ingela; Ruiz-Shulcloper, Jose

Part of Pattern Recognition Letters, p. 82-83, 2021

• DOI for Editorial of special section on CIARP 2019

Learning Cell Nuclei Segmentation Using Labels Generated with Classical Image Analysis Methods

Matuszewski, Damian J.; Ranefall, Petter

Part of Proceedings of the WSCG 2021, p. 335-338, 2021

• DOI for Learning Cell Nuclei Segmentation Using Labels Generated with Classical Image Analysis Methods

Adaptive Mathematical Morphology on Irregularly Sampled Signals in Two Dimensions

Asplund, Teo; Luengo Hendriks, Cris L.; Thurley, Matthew J.; Strand, Robin

Part of Mathematical Morphology - Theory and Applications, p. 108-126, 2020

• DOI for Adaptive Mathematical Morphology on Irregularly Sampled Signals in Two Dimensions
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CoMIR: Contrastive Multimodal Image Representation for Registration

Pielawski, Nicolas; Wetzer, Elisabeth; Öfverstedt, Johan; Lu, Jiahao et al.

Part of NeurIPS - 34th Conference on Neural Information Processing Systems, 2020

A Deep Learning Based Pipeline for Efficient Oral Cancer Screening on Whole Slide Images

Lu, Jiahao; Sladoje, Natasa; Runow Stark, Christina; Darai Ramqvist, Eva et al.

Part of Image Analysis and Recognition, p. 249-261, 2020

• DOI for A Deep Learning Based Pipeline for Efficient Oral Cancer Screening on Whole Slide Images

When texture matters: Texture-focused CNNs outperform general data augmentation and pretraining in oral cancer detection

Wetzer, Elisabeth; Gay, Jo; Harlin, Hugo; Lindblad, Joakim et al.

Part of 2020 IEEE 17th International Symposium on Biomedical Imaging (ISBI), p. 517-521, 2020

• DOI for When texture matters: Texture-focused CNNs outperform general data augmentation and pretraining in oral cancer detection

Fast graph-cut based optimization for practical dense deformable registration of volume images

Ekström, Simon; Malmberg, Filip; Ahlström, Håkan; Kullberg, Joel et al.

Part of Computerized Medical Imaging and Graphics, 2020

• DOI for Fast graph-cut based optimization for practical dense deformable registration of volume images

Bootstrapping Weakly Supervised Segmentation-free Word Spotting through HMM-based Alignment

Wilkinson, Tomas; Nettelblad, Carl

Part of 2020 17th International Conference on Frontiers in Handwriting Recognition (ICFHR), p. 49-54, 2020

• DOI for Bootstrapping Weakly Supervised Segmentation-free Word Spotting through HMM-based Alignment

zOPT: an open source optical projection tomography system and methods for rapid 3D zebrafish imaging

Zhang, Hanqing; Waldmann, Laura; Manuel, Remy; Boije, Henrik et al.

Part of Biomedical Optics Express, p. 4290-4305, 2020

• DOI for zOPT: an open source optical projection tomography system and methods for rapid 3D zebrafish imaging
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Large-scale biometry with interpretable neural network regression on UK Biobank body MRI

Langner, Taro; Strand, Robin; Ahlström, Håkan; Kullberg, Joel

Part of Scientific Reports, 2020

• DOI for Large-scale biometry with interpretable neural network regression on UK Biobank body MRI
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BIAFLOWS: A Collaborative Framework to Reproducibly Deploy and Benchmark Bioimage Analysis Workflows.

Rubens, Ulysse; Mormont, Romain; Paavolainen, Lassi; Bäcker, Volker et al.

Part of Patterns (New York, N.Y.), 2020

• DOI for BIAFLOWS: A Collaborative Framework to Reproducibly Deploy and Benchmark Bioimage Analysis Workflows.
• Download full text (pdf) of BIAFLOWS: A Collaborative Framework to Reproducibly Deploy and Benchmark Bioimage Analysis Workflows.

Stochastic Distance Transform: Theory, Algorithms and Applications

Öfverstedt, Johan; Lindblad, Joakim; Sladoje, Natasa

Part of Journal of Mathematical Imaging and Vision, p. 751-769, 2020

• DOI for Stochastic Distance Transform: Theory, Algorithms and Applications
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Visualisation of 3D Property Data and Assessment of the Impact of Rendering Attributes

Seipel, Stefan; Andrée, Martin; Larsson, Karolina; Paasch, Jesper M. et al.

Part of Journal of Geovisualization and Spatial Analysis, 2020

• DOI for Visualisation of 3D Property Data and Assessment of the Impact of Rendering Attributes
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Large-scale Inference of Liver Fat with Neural Networks on UK Biobank Body MRI

Langner, Taro; Strand, Robin; Ahlström, Håkan; Kullberg, Joel

Part of International Conference on Medical Image Computing and Computer-Assisted Intervention (MICCAI) 2020, p. 602-611, 2020

• DOI for Large-scale Inference of Liver Fat with Neural Networks on UK Biobank Body MRI

Cross-modal Representation Learning for Efficient Registration of Multiphoton and Brightfield Microscopy Images of Skin Tissue

Wetzer, Elisabeth; Pielawski, Nicolas; Öfverstedt, Johan; Jiahao, Lu et al.

Part of 4th NEUBIAS Conference, Bordeaux, France, 2020

Large-scale inference of liver fat with neural networks on UK Biobank body MRI

Langner, Taro; Strand, Robin; Ahlström, Håkan; Kullberg, Joel

Part of Lecture Notes in Computer Science LNCS Vol. 12265, pages 602-611, Springer, Cham., p. 602-611, 2020

Clustered Grid Cell Data Structure for Isosurface Rendering

Nysjö, Fredrik

Part of Journal of WSCG, p. 9-17, 2020

• DOI for Clustered Grid Cell Data Structure for Isosurface Rendering

Two Polynomial Time Graph Labeling Algorithms Optimizing Max-Norm-Based Objective Functions

Malmberg, Filip; Ciesielski, Krzysztof Chris Ciesielski

Part of Journal of Mathematical Imaging and Vision, p. 737-750, 2020

• DOI for Two Polynomial Time Graph Labeling Algorithms Optimizing Max-Norm-Based Objective Functions

Detection of pulmonary micronodules in computed tomography images and false positive reduction using 3D convolutional neural networks

Gupta, Anindya; Saar, Tonis; Martens, Olev; Le Moullec, Yannick et al.

Part of International journal of imaging systems and technology (Print), p. 327-339, 2020

• DOI for Detection of pulmonary micronodules in computed tomography images and false positive reduction using 3D convolutional neural networks

A fast instance selection method for support vector machines in building extraction

Aslani, Mohammad; Seipel, Stefan

Part of Applied Soft Computing, 2020

• DOI for A fast instance selection method for support vector machines in building extraction
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Uncovering hidden reasoning of convolutional neural networks in biomedical image classification by using attribution methods

Koriakina, Nadezhda; Sladoje, Natasa; Wetzer, Elisabeth; Lindblad, Joakim

Part of 4th NEUBIAS Conference, Bordeaux, France, 2020

HISTOBREAST: a collection of brightfield microscopy images of Haematoxylin and Eosin stained breast tissue

Buga, Roxana M.; Totu, Tiberiu; Dumitru, Adrian; Costache, Mariana et al.

Part of Scientific Data, 2020

• DOI for HISTOBREAST: a collection of brightfield microscopy images of Haematoxylin and Eosin stained breast tissue
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Recent Advances in Large Scale Whole Body MRI Image Analysis – Imiomics

Strand, Robin; Ekström, Simon; Breznik, Eva; Sjöholm, Therese et al.

Part of In Proceedings of The 5th International Conference on Sustainable Information Engineering and Technology (SIET 2020), Malang, Indonesia, 2020

Patient-specific fine-tuning of CNNs for follow-up lesion quantification

Jansen, Marielle J A; Kuijf, Hugo J; Kumar Dhara, Ashis; Weaver, Nick A et al.

Part of Journal of Medical Imaging, 2020

Generalised deep learning framework for HEp-2 cell recognition using local binary pattern maps

Bajic, Buda; Majtner, Tomas; Lindblad, Joakim; Sladoje, Natasa

Part of IET Image Processing, p. 1201-1208, 2020

• DOI for Generalised deep learning framework for HEp-2 cell recognition using local binary pattern maps

RayCaching: Amortized Isosurface Rendering for Virtual Reality

Nysjö, Fredrik; Malmberg, Filip; Nyström, Ingela

Part of Computer graphics forum (Print), p. 220-230, 2020

• DOI for RayCaching: Amortized Isosurface Rendering for Virtual Reality
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Learning Socially Appropriate Robot Approaching Behavior Toward Groups using Deep Reinforcement Learning

Gao, Alex Yuan; Yang, Fangkai; Frisk, Martin; Hernandez, Daniel et al.

Part of 2019 28th IEEE International Conference On Robot And Human Interactive Communication (RO-MAN), 2019

• DOI for Learning Socially Appropriate Robot Approaching Behavior Toward Groups using Deep Reinforcement Learning

Facilitating Ultrastructural Pathology through Automated Imaging and Analysis

Sintorn, Ida-Maria; Suveer, Amit; Dragomir, Anca; Hultenby, Kjell et al.

Part of Journal of Pathology Informatics, p. 38-39, 2019

Region-by-region analysis of PET, MRI, and histology in en bloc-resected oligodendrogliomas reveals intra-tumoral heterogeneity

Roodakker, Kenney Roy; Alhuseinalkhudhur, Ali; Al-Jaff, Mohammed; Georganaki, Maria et al.

Part of European Journal of Nuclear Medicine and Molecular Imaging, p. 569-579, 2019

• DOI for Region-by-region analysis of PET, MRI, and histology in en bloc-resected oligodendrogliomas reveals intra-tumoral heterogeneity

Average volume reference space for large scale registration of whole-body magnetic resonance images

Pilia, Martino; Kullberg, Joel; Ahlström, Håkan; Malmberg, Filip et al.

Part of PLOS ONE, 2019

• DOI for Average volume reference space for large scale registration of whole-body magnetic resonance images
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Towards automated multiscale imaging and analysis in TEM: Glomerulus detection by fusion of CNN and LBP maps

Wetzer, Elisabeth; Lindblad, Joakim; Sintorn, Ida-Maria; Hultenby, Kjell et al.

Part of Computer Vision, p. 465-475, 2019

• DOI for Towards automated multiscale imaging and analysis in TEM: Glomerulus detection by fusion of CNN and LBP maps

A whole-body FDG PET/MR atlas for multiparametric voxel-based analysis

Sjöholm, Therese; Ekström, Simon; Strand, Robin; Ahlström, Håkan et al.

Part of Scientific Reports, 2019

• DOI for A whole-body FDG PET/MR atlas for multiparametric voxel-based analysis
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Modeling spatial correlation of transcripts with application to developing pancreas

Liu, Ruishan; Mignardi, Marco; Jones, Robert; Enge, Martin et al.

Part of Scientific Reports, 2019

• DOI for Modeling spatial correlation of transcripts with application to developing pancreas

Super-resolution Reconstruction of Transmission Electron Microscopy Images using Deep Learning

Suveer, Amit; Gupta, Anindya; Kylberg, Gustaf; Sintorn, Ida-Maria

Part of 2019 IEEE 16th International Symposium on Biomedical Imaging (ISBI 2019), p. 548-551, 2019

• DOI for Super-resolution Reconstruction of Transmission Electron Microscopy Images using Deep Learning

Deep Learning in Image Cytometry: A Review

Gupta, Anindya; Harrison, Philip J.; Wieslander, Håkan; Pielawski, Nicolas et al.

Part of Cytometry Part A, p. 366-380, 2019

• DOI for Deep Learning in Image Cytometry: A Review
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Fast and Robust Symmetric Image Registration Based on Distances Combining Intensity and Spatial Information

Öfverstedt, Johan; Lindblad, Joakim; Sladoje, Natasa

Part of IEEE Transactions on Image Processing, p. 3584-3597, 2019

• DOI for Fast and Robust Symmetric Image Registration Based on Distances Combining Intensity and Spatial Information
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Optimization of max-norm objective functions in image processing and computer vision

Malmberg, Filip; Ciesielski, Krzysztof Chris; Strand, Robin

Part of Discrete Geometry for Computer Imagery, p. 206-218, 2019

• DOI for Optimization of max-norm objective functions in image processing and computer vision

Stochastic Distance Transform

Öfverstedt, Johan; Lindblad, Joakim; Sladoje, Natasa

Part of Discrete Geometry for Computer Imagery, p. 75-86, 2019

• DOI for Stochastic Distance Transform

Distance Transform Based on Weight Sequences

Nagy, Benedek; Strand, Robin; Normand, Nicolas

Part of DGCI 2019: Discrete Geometry for Computer Imagery, p. 62-74, 2019

• DOI for Distance Transform Based on Weight Sequences

CNNs on Graphs: A New Pooling Approach and Similarities to Mathematical Morphology

Asplund, Teo; Bengtsson Bernander, Karl; Breznik, Eva

2019

Segmentation of Post-operative Glioblastoma in MRI by U-Net with Patient-specific Interactive Refinement

Dhara, Ashis Kumar; Ayyalasomayajula, Kalyan Ram; Arvids, Erik; Fahlström, Markus et al.

Part of Brainlesion, p. 115-122, 2019

• DOI for Segmentation of Post-operative Glioblastoma in MRI by U-Net with Patient-specific Interactive Refinement

Conventional analysis of movement on non-flat surfaces like the plasma membrane makes Brownian motion appear anomalous

Adler, Jeremy; Sintorn, Ida-Maria; Strand, Robin; Parmryd, Ingela

Part of Communications Biology, 2019

• DOI for Conventional analysis of movement on non-flat surfaces like the plasma membrane makes Brownian motion appear anomalous

On the Effectiveness of Generative Adversarial Networks as HEp-2 Image Augmentation Tool

Majtner, Tomáš; Bajić, Buda; Lindblad, Joakim; Sladoje, Natasa et al.

Part of Scandinavian Conference on Image Analysis, p. 439-451, 2019

• DOI for On the Effectiveness of Generative Adversarial Networks as HEp-2 Image Augmentation Tool

Embedded Prototype Subspace Classification: A subspace learning framework

Hast, Anders; Lind, Mats; Vats, Ekta

Part of Computer Analysis of Images and Patterns, CAIP 2019, PT II, p. 581-592, 2019

• DOI for Embedded Prototype Subspace Classification: A subspace learning framework

Mathematical Morphology on Irregularly Sampled Data Applied to Segmentation of 3D Point Clouds of Urban Scenes

Asplund, Teo; Serna, Andrés; Marcotegui, Beatriz; Strand, Robin et al.

Part of International Symposium on Mathematical Morphology and Its Applications to Signal and Image Processing, 2019

• DOI for Mathematical Morphology on Irregularly Sampled Data Applied to Segmentation of 3D Point Clouds of Urban Scenes

New Definition of Quality-Scale Robustness for Image Processing Algorithms, with Generalized Uncertainty Modeling, Applied to Denoising and Segmentation

Vacavant, Antoine; Lebre, Marie-Ange; Rositi, Hugo; Grand-Brochier, Manuel et al.

Part of RRPR 2018: Reproducible Research in Pattern Recognition, p. 138-149, 2019

• DOI for New Definition of Quality-Scale Robustness for Image Processing Algorithms, with Generalized Uncertainty Modeling, Applied to Denoising and Segmentation

Progress in Pattern Recognition, Image Analysis, Computer Vision, and Applications

Nyström, Ingela; Heredia, Yanio Hernández; Núñez, Vladimir Milián

2019

Towards automated multiscale Glomeruli detection and analysis in TEM by fusion of CNN and LBP maps

Wetzer, Elisabeth; Lindblad, Joakim; Sintorn, Ida-Maria; Hultenby, Kjell et al.

Part of 3rd NEUBIAS Conference, 2019

Training-Free and Segmentation-Free Word Spotting using Feature Matching and Query Expansion

Vats, Ekta; Hast, Anders; Fornés, Alicia

Part of Proc. 15th International Conference on Document Analysis and Recognition, 2019

Robust Symmetric Affine Image Registration

Öfverstedt, Johan; Lindblad, Joakim; Sladoje, Natasa

Part of Swedish Symposium on Image Analysis, 2019

Stochastic Distance Functions with Applications in Object Detection and Image Segmentation

Öfverstedt, Johan; Lindblad, Joakim; Sladoje, Natasa

Part of Swedish Symposium on Image Analysis, 2019

Oral Cancer Detection: A Comparison of Texture Focused Deep Learning Approaches

Gay, Jo; Harlin, Hugo; Wetzer, Elisabeth; Lindblad, Joakim et al.

Part of Proceedings of the Swedish Society for Automated Image Analysis (SSBA), 2019

Sparsity promoting super-resolution coverage segmentation by linear unmixing in presence of blur and noise

Bajic, Buda; Lindblad, Joakim; Sladoje, Natasa

Part of Journal of Electronic Imaging (JEI), 2019

• DOI for Sparsity promoting super-resolution coverage segmentation by linear unmixing in presence of blur and noise

A strategy for OCT estimation of the optic nerve head pigment epithelium central limit-inner limit of the retina minimal distance, PIMD-2π

Sandberg Melin, Camilla; Malmberg, Filip; Söderberg, Per G.

Part of Acta Ophthalmologica, p. 208-213, 2019

• DOI for A strategy for OCT estimation of the optic nerve head pigment epithelium central limit-inner limit of the retina minimal distance, PIMD-2π

Glandular Segmentation of Prostate Cancer: An Illustration of How the Choice of Histopathological Stain Is One Key to Success for Computational Pathology

Avenel, Christophe; Tolf, Anna; Dragomir, Anca; Carlbom, Ingrid

Part of Frontiers in Bioengineering and Biotechnology, 2019

• DOI for Glandular Segmentation of Prostate Cancer: An Illustration of How the Choice of Histopathological Stain Is One Key to Success for Computational Pathology
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Visualization of convolutional neural network class activations in automated oral cancer detection for interpretation of malignancy associated changes

Koriakina, Nadezhda; Sladoje, Natasa; Bengtsson, Ewert; Ramqvist, Eva Darai et al.

Part of 3rd NEUBIAS Conference, Luxembourg, 2-8 February 2019, 2019

Texture-based oral cancer detection: A performance analysis of deep learning approaches.

Gay, Jo; Harlin, Hugo; Wetzer, Elisabeth; Lindblad, Joakim et al.

Part of 3rd NEUBIAS Conference, 2019

A robust multi-variability model based liver segmentation algorithm for CT-scan and MRI modalities

Lebre, Marie-Ange; Vacavant, Antoine; Grand-Brochier, Manuel; Rositi, Hugo et al.

Part of Computerized Medical Imaging and Graphics, 2019

• DOI for A robust multi-variability model based liver segmentation algorithm for CT-scan and MRI modalities

Rational nanotoolbox with theranostic potential for medicated pro-regenerative corneal implants

Patra, Hirak K.; Azharuddin, Mohammad; Islam, Mohammad M.; Papapavlou, Georgia et al.

Part of Advanced Functional Materials, 2019

• DOI for Rational nanotoolbox with theranostic potential for medicated pro-regenerative corneal implants

Brown adipose tissue estimated with the magnetic resonance imaging fat fraction is associated with glucose metabolism in adolescents

Lundström, Elin; Ljungberg, Joy; Andersson, Jonathan; Manell, Hannes et al.

Part of Pediatric Obesity, 2019

• DOI for Brown adipose tissue estimated with the magnetic resonance imaging fat fraction is associated with glucose metabolism in adolescents

Relationship between endothelium-dependent vasodilation and fat distribution using the new "imiomics" image analysis technique

Lind, Lars; Strand, Robin; Michaëlsson, Karl; Kullberg, Joel et al.

Part of NMCD. Nutrition Metabolism and Cardiovascular Diseases, p. 1077-1086, 2019

• DOI for Relationship between endothelium-dependent vasodilation and fat distribution using the new "imiomics" image analysis technique
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Image analysis in digital pathology: Combining automated assessment of Ki67 staining quality with calculation of Ki67 cell proliferation index

Bengtsson, Ewert; Ranefall, Petter

Part of Cytometry Part A, p. 714-716, 2019

• DOI for Image analysis in digital pathology: Combining automated assessment of Ki67 staining quality with calculation of Ki67 cell proliferation index

Tracking Microscope Performance: A Workflow to Compare Point Spread Function Evaluations Over Time

Klemm, Anna H.; Thomae, Andreas W.; Wachal, Katarina; Dietzel, Steffen

Part of Microscopy and Microanalysis, p. 699-704, 2019

• DOI for Tracking Microscope Performance: A Workflow to Compare Point Spread Function Evaluations Over Time

Capturing and characterizing human activities using building locations in America

Ren, Zheng; Jiang, Bin; Seipel, Stefan

Part of ISPRS International Journal of Geo-Information, 2019

• DOI for Capturing and characterizing human activities using building locations in America

Special Section on Image Cytometry

Bengtsson, Ewert; Tárnok, Attila

Part of Cytometry Part A, p. 363-365, 2019

• DOI for Special Section on Image Cytometry

Content-Based Image Retrieval System for Pulmonary Nodules Using Optimal Feature Sets and Class Membership-Based Retrieval

Mehre, Shrikant A.; Dhara, Ashis Kumar; Garg, Mandeep; Kalra, Naveen et al.

Part of Journal of digital imaging, p. 362-385, 2019

• DOI for Content-Based Image Retrieval System for Pulmonary Nodules Using Optimal Feature Sets and Class Membership-Based Retrieval

PDNet: Semantic segmentation integrated with a primal-dual network for document binarization

Ayyalasomayajula, Kalyan Ram; Malmberg, Filip; Brun, Anders

Part of Pattern Recognition Letters, p. 52-60, 2019

• DOI for PDNet: Semantic segmentation integrated with a primal-dual network for document binarization
• Download full text (pdf) of PDNet: Semantic segmentation integrated with a primal-dual network for document binarization

Correcting exorbitism by monobloc frontofacial advancement in Crouzon–Pfeiffer syndrome: An age-specific, time-related, controlled study

Way, Benjamin L. M.; Khonsari, Roman H.; Karunakaran, Tharsika; Nysjö, Johan et al.

Part of Plastic and reconstructive surgery (1963), 2019

• DOI for Correcting exorbitism by monobloc frontofacial advancement in Crouzon–Pfeiffer syndrome: An age-specific, time-related, controlled study

Creating an Atlas over Handwritten Script Signs

Hast, Anders; Mårtensson, Lasse; Vats, Ekta; Heil, Raphaela

Part of Digital Humanities in the Nordic Countries, 2019

Making large collections of handwritten material easily accessible and searchable

Hast, Anders; Cullhed, Per; Vats, Ekta; Abrate, Matteo

Part of Digital Libraries, p. 18-28, 2019

• DOI for Making large collections of handwritten material easily accessible and searchable

In search of the scribe: Letter spotting as a tool for identifying scribes in large handwritten text corpora

Mårtensson, Lasse; Vats, Ekta; Hast, Anders; Fornés, Alicia

Part of Human IT, p. 95-120, 2019

When Can lp-norm Objective Functions Be Minimized via Graph Cuts?

Malmberg, Filip; Strand, Robin

Part of Combinatorial Image Analysis, p. 112-117, 2018

• DOI for When Can lp-norm Objective Functions Be Minimized via Graph Cuts?

SoftCut: A Virtual Planning Tool for Soft Tissue Resection on CT Images

Blache, Ludovic; Nysjö, Fredrik; Malmberg, Filip; Thor, Andreas et al.

Part of Medical Image Understanding and Analysis, p. 299-310, 2018

• DOI for SoftCut: A Virtual Planning Tool for Soft Tissue Resection on CT Images

Visual GISwaps: an interactive visualization framework for geospatial decision making

Milutinovic, Goran; Seipel, Stefan

Part of Proc. 13th International Joint Conference on Computer Vision, Imaging and Computer Graphics Theory and Applications, p. 236-243, 2018

• DOI for Visual GISwaps: an interactive visualization framework for geospatial decision making

Segmentation of Lung Field in HRCT Images Using U-Net Based Fully Convolutional Networks

Kumar, Abhishek; Agarwala, Sunita; Dhara, Ashis Kumar; Nandi, Debashis et al.

Part of Medical Image Understanding and Analysis, p. 84-93, 2018

• DOI for Segmentation of Lung Field in HRCT Images Using U-Net Based Fully Convolutional Networks

Quantitative image analysis of protein expression and colocalisation in skin sections

Zhang, Hanqian; Ericsson, Maja; Virtanen, Marie; Weström, Simone et al.

Part of Experimental dermatology, p. 196-199, 2018

• DOI for Quantitative image analysis of protein expression and colocalisation in skin sections

Detection of Malignancy-Associated Changes Due to Precancerous and Oral Cancer Lesions: A Pilot Study Using Deep Learning

Bengtsson, Ewert; Wieslander, Håkan; Forslid, Gustav; Wählby, Carolina et al.

Part of CYTO2018, 2018

Brush Biopsy For HR-HPV Detection With FTA Card And AI For Cytology Analysis - A Viable Non-invasive Alternative

Runow Stark, Christina; Gustavsson, Inger M.; Gyllensten, Ulf B.; Darai Ramqvist, Eva et al.

Part of EAOM2018, 2018

Whole Slide Image Registration for the Study of Tumor Heterogeneity

Solorzano, Leslie; Almeida, Gabriela; Mesquita, Bárbara; Martins, Diana et al.

Part of MICCAI 2018 - International Workshop on Ophthalmic Medical Image Analysis, p. 95-102, 2018

• DOI for Whole Slide Image Registration for the Study of Tumor Heterogeneity

Image-Based Detection of Patient-Specific Drug-Induced Cell-Cycle Effects in Glioblastoma

Matuszewski, Damian J.; Wählby, Carolina; Krona, Cecilia; Nelander, Sven et al.

Part of SLAS Discovery: Advancing Life Sciences R&D, p. 1030-1039, 2018

• DOI for Image-Based Detection of Patient-Specific Drug-Induced Cell-Cycle Effects in Glioblastoma

Finish line distinctness and accuracy in 7 intraoral scanners versus conventional impression: an in vitro descriptive comparison

Nedelcu, Robert; Olsson, Pontus; Nyström, Ingela; Thor, Andreas

Part of BMC Oral Health, 2018

• DOI for Finish line distinctness and accuracy in 7 intraoral scanners versus conventional impression: an in vitro descriptive comparison

Minimal annotation training for segmentation of microscopy images

Matuszewski, Damian J.; Sintorn, Ida-Maria

Part of Proc. 15th International Symposium on Biomedical Imaging, p. 387-390, 2018

• DOI for Minimal annotation training for segmentation of microscopy images

BIM and 3D property visualisation

Andrée, Martin; Paasch, Jesper M.; Paulsson, Jenny; Seipel, Stefan

Part of Proc. FIG Congress 2018, 2018

Learning surrogate models of document image quality metrics for automated document image processing

Singh, Prashant; Vats, Ekta; Hast, Anders

Part of Proc. 13th IAPR International Workshop on Document Analysis Systems, p. 67-72, 2018

• DOI for Learning surrogate models of document image quality metrics for automated document image processing

Denoising of short exposure transmission electron microscopy images for ultrastructural enhancement

Bajic, Buda; Suveer, Amit; Gupta, Anindya; Pepic, Ivana et al.

Part of Proc. 15th International Symposium on Biomedical Imaging, p. 921-925, 2018

• DOI for Denoising of short exposure transmission electron microscopy images for ultrastructural enhancement

Towards automated multiscale imaging and analysis in TEM: Glomeruli detection by fusion of CNN and LBP maps

Wetzer, Elisabeth; Lindblad, Joakim; Sintorn, Ida-Maria; Hultenby, Kjell et al.

Part of Swedish Symposium on Deep Learning, 2018

An intelligent user interface for efficient semi-automatic transcription of historical handwritten documents

Hast, Anders; Vats, Ekta

Part of Proc. 23rd International Conference on Intelligent User Interfaces Companion, 2018

• DOI for An intelligent user interface for efficient semi-automatic transcription of historical handwritten documents

Distance Between Vector-valued Images based on Intersection Decomposition with Applications in Object Detection

Öfverstedt, Johan; Sladoje, Natasa; Lindblad, Joakim

Part of Swedish Symposium on Image Analysis, 2018

Denoising of Short Exposure Transmission Electron Microscopy Images using CNN

Gupta, Anindya; Suveer, Amit; Bajic, Buda; Pepic, Ivana et al.

Part of Swedish Symposium on Image Analysis, 2018

Comparison analysis of orbital shape and volume in unilateral fractured orbits

Nilsson, Johanna; Nysjö, Johan; Carlsson, Anders-Petter; Thor, Andreas

Part of Journal of Cranio-Maxillofacial Surgery, p. 381-387, 2018

• DOI for Comparison analysis of orbital shape and volume in unilateral fractured orbits

Interactive segmentation of glioblastoma for post-surgical treatment follow-up

Dhara, Ashis Kumar; Arids, Erik; Fahlström, Markus; Wikström, Johan et al.

Part of Proc. 24th International Conference on Pattern Recognition, p. 1199-1204, 2018

• DOI for Interactive segmentation of glioblastoma for post-surgical treatment follow-up

GISwaps: A new method for decision making in continuous choice models based on even swaps

Milutinovic, Goran; Ahonen-Jonnarth, Ulla; Seipel, Stefan

Part of International Journal of Decision Support System Technology, p. 57-78, 2018

• DOI for GISwaps: A new method for decision making in continuous choice models based on even swaps
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Exploring the Applicability of Capsule Networks for WordSpotting in Historical Handwritten Manuscripts

Heil, Raphaela; Vats, Ekta; Hast, Anders

2018

Word Spotting in Historical Handwritten Manuscripts using Capsule Networks

Heil, Raphaela; Vats, Ekta; Hast, Anders

2018

The Effect of DMPA Use on the Human Cervical Epithelium: Mechanisms Revealed by Image Analysis

Edfeldt, Gabriella; Lajoie, Julie; Röhl, Maria; Omollo, Kenneth et al.

Part of AIDS Research and Human Retroviruses, p. 310-310, 2018

The Scarcity of Universal Colour Names

Borgefors, Gunilla

Part of Proceedings of 7th International Conference on Pattern Recognition Applications and Methods (ICPRAM 2018), p. 496-502, 2018

• DOI for The Scarcity of Universal Colour Names

An Objective Scoring Framework for Histology Slide Image Mosaics Applicable for the Reliable Benchmarking of Image Quality Assessment Algorithms

Totu, Tiberiu; Buga, Roxana; Dumitru, Adrian; Costache, Mariana et al.

Part of IEEE Access, p. 53080-53091, 2018

• DOI for An Objective Scoring Framework for Histology Slide Image Mosaics Applicable for the Reliable Benchmarking of Image Quality Assessment Algorithms

Automatic detection of multisize pulmonary nodules in CT images: Large-scale validation of the false-positive reduction step

Gupta, Anindya; Saar, Tonis; Martens, Olev; Le Moullec, Yannick

Part of Medical physics (Lancaster), p. 1135-1149, 2018

• DOI for Automatic detection of multisize pulmonary nodules in CT images: Large-scale validation of the false-positive reduction step

Extracting script features from a large corpus of handwritten documents

Vats, Ekta; Hast, Anders; Mårtensson, Lasse

Part of Digital Humanities in the Nordic Countries, 2018

Multiplexed fluorescence microscopy reveals heterogeneity among stromal cells in mouse bone marrow sections

Holzwarth, Karolin; Köhler, Ralf; Philipsen, Lars; Tokoyoda, Koji et al.

Part of Cytometry Part A, p. 876-888, 2018

• DOI for Multiplexed fluorescence microscopy reveals heterogeneity among stromal cells in mouse bone marrow sections

TexT – Text extractor tool for handwritten document transcription and annotation

Hast, Anders; Cullhed, Per; Vats, Ekta

Part of Digital Libraries and Multimedia Archives, p. 81-92, 2018

• DOI for TexT – Text extractor tool for handwritten document transcription and annotation

Human Immunodeficiency Virus-Infected Women Have High Numbers of CD103^-CD8⁺ T Cells Residing Close to the Basal Membrane of the Ectocervical Epithelium

Gibbs, Anna; Buggert, Marcus; Edfeldt, Gabriella; Ranefall, Petter et al.

Part of Journal of Infectious Diseases, p. 453-465, 2018

• DOI for Human Immunodeficiency Virus-Infected Women Have High Numbers of CD103^-CD8⁺ T Cells Residing Close to the Basal Membrane of the Ectocervical Epithelium

Radial line Fourier descriptor for historical handwritten text representation

Hast, Anders; Vats, Ekta

Part of Proc. 26th International Conference on Computer Graphics, 2018

Localization of lung fields in HRCT images using a deep convolution neural network

Kumar, Abhishek; Agarwala, Sunita; Dhara, Ashis Kumar; Mukhopadhyay, Sudipta et al.

Part of Medical Imaging 2018, 2018

• DOI for Localization of lung fields in HRCT images using a deep convolution neural network

Radial line Fourier descriptor for historical handwritten text representation

Hast, Anders; Vats, Ekta

Part of Journal of WSCG, p. 31-40, 2018

• DOI for Radial line Fourier descriptor for historical handwritten text representation

A fast Fourier based feature descriptor and a cascade nearest neighbour search with an efficient matching pipeline for mosaicing of microscopy images

Hast, Anders; Sablina, Victoria A.; Sintorn, Ida-Maria; Kylberg, Gustaf

Part of Pattern Recognition and Image Analysis, p. 261-272, 2018

• DOI for A fast Fourier based feature descriptor and a cascade nearest neighbour search with an efficient matching pipeline for mosaicing of microscopy images

Workshop on Robots for Learning-R4L

Johal, Wafa; Vogt, Paul; Kennedy, James; de Haas, Mirjam et al.

Part of HRI '17, p. 423-424, 2017

• DOI for Workshop on Robots for Learning-R4L

Exploring the link between self-assessed mimicry and embodiment in HRI

Paetzel, Maike; Hupont, Isabelle; Varni, Giovanna; Chetouani, Mohamed et al.

Part of Proc. Companion of 12th ACM/IEEE International Conference on Human-Robot Interaction, p. 245-246, 2017

• DOI for Exploring the link between self-assessed mimicry and embodiment in HRI

Classification of cross-sections for vascular skeleton extraction using convolutional neural networks

Lidayová, Kristína; Gupta, Anindya; Frimmel, Hans; Sintorn, Ida-Maria et al.

Part of Medical Image Understanding and Analysis, p. 182-194, 2017

• DOI for Classification of cross-sections for vascular skeleton extraction using convolutional neural networks

A multidimensional perspective on the uncanny valley effect: Studying the interplay between a robot's appearance and interaction strategy

Paetzel, Maike

Part of Proc. Companion of 12th ACM/IEEE International Conference on Human-Robot Interaction, p. 363-364, 2017

• DOI for A multidimensional perspective on the uncanny valley effect: Studying the interplay between a robot's appearance and interaction strategy

Automated training of deep convolutional neural networks for cell segmentation

Kecheril Sadanandan, Sajith; Ranefall, Petter; Le Guyader, Sylvie; Wählby, Carolina

Part of Scientific Reports, 2017

• DOI for Automated training of deep convolutional neural networks for cell segmentation
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Automated segmentation of human cervical-supraclavicular adipose tissue in magnetic resonance images

Lundström, Elin; Strand, Robin; Forslund, Anders; Bergsten, Peter et al.

Part of Scientific Reports, 2017

• DOI for Automated segmentation of human cervical-supraclavicular adipose tissue in magnetic resonance images
• Download full text (pdf) of Automated segmentation of human cervical-supraclavicular adipose tissue in magnetic resonance images

Deep convolutional neural networks for detecting cellular changes due to malignancy

Wieslander, Håkan; Forslid, Gustav; Bengtsson, Ewert; Wählby, Carolina et al.

Part of Proc. 16th International Conference on Computer Vision Workshops, p. 82-89, 2017

• DOI for Deep convolutional neural networks for detecting cellular changes due to malignancy

The Boolean Map Distance: Theory and Efficient Computation

Malmberg, Filip; Strand, Robin; Zhang, Jianming; Sclaroff, Stan

Part of International Conference on Discrete Geometry for Computer Imagery, p. 335-346, 2017

• DOI for The Boolean Map Distance: Theory and Efficient Computation

A concept for holistic whole body MRI data analysis, Imiomics

Strand, Robin; Malmberg, Filip; Johansson, Lars; Lind, Lars et al.

Part of PLOS ONE, 2017

• DOI for A concept for holistic whole body MRI data analysis, Imiomics
• Download full text (pdf) of A concept for holistic whole body MRI data analysis, Imiomics

Using anti-aliased signed distance fields for generating surgical guides and plates from CT images

Nysjö, Fredrik; Olsson, Pontus; Malmberg, Filip; Carlbom, Ingrid B. et al.

Part of Journal of WSCG, p. 11-20, 2017

• Download full text (pdf) of Using anti-aliased signed distance fields for generating surgical guides and plates from CT images

Convolutional neural networks for false positive reduction of automatically detected cilia in low magnification TEM images

Gupta, Anindya; Suveer, Amit; Lindblad, Joakim; Dragomir, Anca et al.

Part of Image Analysis, p. 407-418, 2017

• DOI for Convolutional neural networks for false positive reduction of automatically detected cilia in low magnification TEM images

Enhancement of cilia sub-structures by multiple instance registration and super-resolution reconstruction

Suveer, Amit; Sladoje, Nataša; Lindblad, Joakim; Dragomir, Anca et al.

Part of Image Analysis, p. 362-374, 2017

• DOI for Enhancement of cilia sub-structures by multiple instance registration and super-resolution reconstruction

False positive reduction of cilia detected in low resolution TEM images using a convolutional neural network

Gupta, Anindya; Suveer, Amit; Lindblad, Joakim; Dragomir, Anca et al.

Part of Swedish Symposium on Image Analysis, 2017

• Download full text (pdf) of False positive reduction of cilia detected in low resolution TEM images using a convolutional neural network

Cilia ultrastructural visibility enhancement by multiple instance registration and super-resolution reconstruction

Suveer, Amit; Sladoje, Natasa; Lindblad, Joakim; Dragomir, Anca et al.

Part of Swedish Symposium on Image Analysis, 2017

Mathematical morphology on irregularly sampled data in one dimension

Asplund, Teo; Luengo Hendriks, Cris L.; Thurley, Matthew J.; Strand, Robin

Part of Mathematical Morphology - Theory and Applications, p. 1-24, 2017

• DOI for Mathematical morphology on irregularly sampled data in one dimension

An efficient descriptor based on radial line integration for fast non invariant matching and registration of microscopy images

Hast, Anders; Kylberg, Gustav; Sintorn, Ida-Maria

Part of Advanced Concepts for Intelligent Vision Systems, p. 723-734, 2017

• DOI for An efficient descriptor based on radial line integration for fast non invariant matching and registration of microscopy images

On-the-fly historical handwritten text annotation

Vats, Ekta; Hast, Anders

Part of Proc. 14th IAPR International Conference on Document Analysis and Recognition, p. 10-14, 2017

• DOI for On-the-fly historical handwritten text annotation

Neural Ctrl-F: Segmentation-free query-by-string word spotting in handwritten manuscript collections

Wilkinson, Tomas; Lindström, Jonas; Brun, Anders

Part of 2017 IEEE International Conference on Computer Vision (ICCV), p. 4443-4452, 2017

• DOI for Neural Ctrl-F: Segmentation-free query-by-string word spotting in handwritten manuscript collections
• Download full text (pdf) of Neural Ctrl-F: Segmentation-free query-by-string word spotting in handwritten manuscript collections

Historical document binarization combining semantic labeling and graph cuts

Ayyalasomayajula, Kalyan Ram; Brun, Anders

Part of Image Analysis, p. 386-396, 2017

• DOI for Historical document binarization combining semantic labeling and graph cuts
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Distance between vector-valued fuzzy sets based on intersection decomposition with applications in object detection

Öfverstedt, Johan; Sladoje, Natasa; Lindblad, Joakim

Part of Mathematical Morphology and its Applications to Signal and Image Processing, p. 395-407, 2017

• DOI for Distance between vector-valued fuzzy sets based on intersection decomposition with applications in object detection