Joakim Lindblad
Professor at Department of Information Technology; Vi3; Image Analysis
- Telephone:
- +46 18 471 34 32
- Mobile phone:
- +46 73 316 85 49
- E-mail:
- joakim.lindblad@it.uu.se
- Visiting address:
- Hus 10, Lägerhyddsvägen 1
- Postal address:
- Box 337
751 05 UPPSALA
- Academic merits:
- Docent
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Short presentation
Keywords
- artificial intelligence
- bildanalys
- deep learning
- image analysis
- image registration
- maskininlärning
- pattern recognition
- quantitative microscopy
- shape analysis
Biography
Joakim Lindblad received the M.Sc. in engineering physics and Ph.D. in computerized image analysis from Uppsala University, Sweden, in 1997 and 2003, respectively. He is currently Professor of Computerized Image Processing at the Department of Information Technology, Uppsala University, Sweden; Senior Research Associate at Mathematical Institute of the Serbian Academy of Sciences and Arts, Serbia; and Head of Research at Topgolf Sweden AB, Stockholm, Sweden. His research interests involve development of general and robust methods for image processing and analysis, including data driven approaches such as deep learning, typically within the context of biomedical and medical applications.
Publications
Recent publications
- Let it shine: Autofluorescence of Papanicolaou-stain improves AI-based cytological oral cancer detection (2025)
- Cross-modality sub-image retrieval using contrastive multimodal image representations (2024)
- Detection of Extremely Sparse Key Instances in Whole Slide Cytology Images via Self-supervised One-class Representation Learning (2024)
- Are We Friends (2024)
- Deep multiple instance learning versus conventional deep single instance learning for interpretable oral cancer detection (2024)
All publications
Articles
- Let it shine: Autofluorescence of Papanicolaou-stain improves AI-based cytological oral cancer detection (2025)
- Cross-modality sub-image retrieval using contrastive multimodal image representations (2024)
- Deep multiple instance learning versus conventional deep single instance learning for interpretable oral cancer detection (2024)
- Correlated multimodal imaging in life sciences: lessons learnt (2024)
- Dental hygienists and dentists as providers of brush biopsies for oral mucosa screening (2023)
- A paradigm shift in the prevention and diagnosis of oral squamous cell carcinoma. (2023)
- INSPIRE (2023)
- Early Detection of Oral Potentially Malignant Disorders (2022)
- Is image-to-image translation the panacea for multimodal image registration? (2022)
- Guest Editorial (2022)
- Fast computation of mutual information in the frequency domain with applications to global multimodal image alignment (2022)
- Icke-invasiv kontroll av cellförändringar i munslemhinnan (2021)
- Is Image-to-Image Translation the Panacea for Multimodal Image Registration? A Comparative Study (2021)
- CytoBrowser: a browser-based collaborative annotation platform for whole slide images (2021)
- Cross-Sim-NGF: FFT-Based Global Rigid Multimodal Alignment of Image Volumes using Normalized Gradient Fields (2021)
- Generalised deep learning framework for HEp-2 cell recognition using local binary pattern maps (2020)
- Stochastic Distance Transform (2020)
- Sparsity promoting super-resolution coverage segmentation by linear unmixing in presence of blur and noise (2019)
- A Deep Learning based Pipeline for Efficient Oral Cancer Screening on Whole Slide Images (2019)
- Facilitating Ultrastructural Pathology through Automated Imaging and Analysis (2019)
- Fast and Robust Symmetric Image Registration Based on Distances Combining Intensity and Spatial Information (2019)
- Fast and Robust Symmetric Image Registration Based on Intensity and Spatial Information (2018)
- Restoration of images degraded by signal-dependent noise based on energy minimization (2016)
- Estimation of Feret's diameter from pixel coverage representation of a shape (2016)
- Precise Euclidean distance transforms in 3D from voxel coverage representation (2015)
- Estimation of linear deformations of 2D and 3D fuzzy objects (2015)
- A new set distance and its application to shape registration (2014)
- Linear time distances between fuzzy sets with applications to pattern matching and classification (2014)
- Blind Color Decomposition of Histological Images (2013)
- Coverage segmentation based on linear unmixing and minimization of perimeter and boundary thickness (2012)
- Regularized image denoising based on spectral gradient optimization (2011)
- A Graph-based Framework for Sub-pixel Image Segmentation (2011)
- Measurement of fibre–fibre contact in three-dimensional images of fibrous materials obtained from X-ray synchrotron microtomography (2011)
- Measurement of fibre–fibre contact in three-dimensional images of fibrous materials obtained from X-ray synchrotron microtomography (2011)
- Extracting 3D information on bone remodeling in the proximity of titanium implants in SRμCT image volumes (2011)
- Defuzzification of spatial fuzzy sets by feature distance minimization (2011)
- Effects of aging and gender on the spatial organization of nuclei in single human skeletal muscle cells (2010)
- Role of fibre–fibre and fibre–matrix adhesion in stress transfer in composites made from resin-impregnated paper sheets (2009)
- Effects of ageing and gender on the spatial organization of nuclei in single human skeletal muscle cells (2009)
- Effects of ageing and gender on the spatial organisation of nuclei in single human skeletal muscle cells (2009)
- Myonuclear domain size and myosin isoform expression in muscle fibres from mammals representing a 100 000-fold difference in body size (2009)
- High-precision boundary length estimation by utilizing gray-level information (2009)
- Representation and Reconstruction of Fuzzy Disks by Moments (2007)
- Surface Area Estimation of Digitized 3D Objects using Weighted Local Configurations (2005)
- Robust cell image segmentation methods (2004)
- Image Analysis for Automatic Segmentation of Cytoplasms and Classification of Rac1 Activation (2004)
- Algorithms for cytoplasm segmentation of fluorescence labeled cells (2002)
- A comparison of methods for estimation of intensity nonuniformities in 2D and 3D microscope images of fluorescence stained cells (2001)
- Statistical quality control for segmentation of fluorescence labeled cells (2001)
- Histogram thresholding using kernel density estimates (2000)
- Rotation-Equivariant Semantic Instance Segmentation
- UpStory
- Sensitive key instance detection: Helping a cytotechnologist to find a needle in a haystack
- Can representation learning for multimodal image registration be improved by supervision of intermediate layers?
Books
- Discrete Geometry and Mathematical Morphology (2021)
- Development of Algorithms for Digital Image Cytometry (2002)
Chapters
- Introduction—computer-assisted analysis of multimodal image data (2021)
- Computer-assisted analysis of multimodal image data—perspectives and conclusion (2021)
- The coverage model and its use in image processing (2012)
- Multiple tissue antigen analysis by sequential immunofluorescence staining and multi-dimensional image analysis (2001)
Conferences
- Detection of Extremely Sparse Key Instances in Whole Slide Cytology Images via Self-supervised One-class Representation Learning (2024)
- Are We Friends (2024)
- Investigating the Relevance of Contextual Information Towards Improving Deep CNN Based Oral Cancer Screening on Whole Slide Cytology Samples (2023)
- Multimodal deformable image registration using contrastive learning of equivariant image representations (2023)
- Contrastive Learning of Equivariant Image Representations for Multimodal Deformable Registration (2023)
- Can Representation Learning for Multimodal Image Registration be Improved by Supervision of Intermediate Layers? (2023)
- Partial dimensional collapse in contrastive learning when using intermediate layers (2023)
- End-to-end Multiple Instance Learning with Gradient Accumulation (2022)
- Rotation-Equivariant Semantic Instance Segmentation on Biomedical Images (2022)
- Label-Free Reverse Image Search of Multimodal Microscopy Images (2022)
- DCNN based Oral Cancer Screening using Whole Slide Cytology Images (2022)
- End-to-End Learning and Analysis of Infant Engagement During Guided Play (2022)
- Re-Ranking Strategies in Cross-Modality Microscopy Retrieval (2022)
- Rotationally Equivariant Representation Learning for Multimodal Images (2022)
- Efficient Algorithms for Global Multimodal Image Registration (2022)
- Cross-Sim-NGF: FFT-Based Global Rigid Multimodal Alignment of Image Volumes using Normalized Gradient Fields (2022)
- Replacing data augmentation with rotation-equivariant CNNs in image-based classification of oral cancer (2021)
- Automatic Analysis of Infant Engagement during Play (2021)
- The Effect of Within-Bag Sampling on End-to-End Multiple Instance Learning (2021)
- Image-to-Image Translation in Multimodal Image Registration: How Well Does It Work? (2021)
- Contrastive Learning for Equivariant Multimodal Image Representations (2021)
- Comir: Contrastive multimodal image representation for registration (2021)
- Registration of Multimodal Microscopy Images using CoMIR – learned structural image representations (2021)
- Fast Computation of Mutual Information with Application to Global Multimodal Image Alignment of Micrographs (2021)
- Uncovering hidden reasoning of convolutional neural networks in biomedical image classification by using attribution methods (2020)
- A Deep Learning Based Pipeline for Efficient Oral Cancer Screening on Whole Slide Images (2020)
- CoMIR: Contrastive Multimodal Image Representation for Registration (2020)
- When texture matters (2020)
- Cross-modal Representation Learning for Efficient Registration of Multiphoton and Brightfield Microscopy Images of Skin Tissue (2020)
- Texture-based oral cancer detection: A performance analysis of deep learning approaches. (2019)
- Oral Cancer Detection: (2019)
- Visualization of convolutional neural network class activations in automated oral cancer detection for interpretation of malignancy associated changes (2019)
- On the Effectiveness of Generative Adversarial Networks as HEp-2 Image Augmentation Tool (2019)
- Towards automated multiscale Glomeruli detection and analysis in TEM by fusion of CNN and LBP maps (2019)
- Towards automated multiscale imaging and analysis in TEM (2019)
- Stochastic Distance Transform (2019)
- Stochastic Distance Functions with Applications in Object Detection and Image Segmentation (2019)
- Robust Symmetric Affine Image Registration (2019)
- Denoising of short exposure transmission electron microscopy images for ultrastructural enhancement (2018)
- Detection of Malignancy-Associated Changes Due to Precancerous and Oral Cancer Lesions: A Pilot Study Using Deep Learning (2018)
- Denoising of Short Exposure Transmission Electron Microscopy Images using CNN (2018)
- Brush Biopsy For HR-HPV Detection With FTA Card And AI For Cytology Analysis - A Viable Non-invasive Alternative (2018)
- Towards automated multiscale imaging and analysis in TEM: Glomeruli detection by fusion of CNN and LBP maps (2018)
- Distance Between Vector-valued Images based on Intersection Decomposition with Applications in Object Detection (2018)
- Decoding gene expression in 2D and 3D (2017)
- False positive reduction of cilia detected in low resolution TEM images using a convolutional neural network (2017)
- Convolutional neural networks for false positive reduction of automatically detected cilia in low magnification TEM images (2017)
- Distance Between Vector-Valued Representations of Objects in Images with Application in Object Detection and Classification (2017)
- Cilia ultrastructural visibility enhancement by multiple instance registration and super-resolution reconstruction (2017)
- Enhancement of cilia sub-structures by multiple instance registration and super-resolution reconstruction (2017)
- Distance between vector-valued fuzzy sets based on intersection decomposition with applications in object detection (2017)
- Single image super-resolution reconstruction in presence of mixed Poisson-Gaussian noise (2016)
- Blind restoration of images degraded with mixed poisson-Gaussian noise with application in transmission electron microscopy (2016)
- Blind deconvolution of images degraded with mixed Poisson-Gaussian noise with application in Transmission Electron Microscopy (2016)
- Signature of a Shape Based on Its Pixel Coverage Representation (2016)
- Automated detection of cilia in low magnification transmission electron microscopy images using template matching (2016)
- αLBP – a novel member of the Local Binary Pattern family based on α-cutting (2015)
- Coverage segmentation of 3D thin structures (2015)
- Microscopy image enhancement for cost-effective cervical cancer screening (2015)
- Exact linear time Euclidean distance transforms of grid line sampled shapes (2015)
- High-resolution reconstruction by feature distance minimization from multiple views of an object (2015)
- An evaluation of potential functions for regularized image deblurring (2014)
- Optimizing optics and imaging for pattern recognition based screening tasks (2014)
- Coverage segmentation of thin structures by linear unmixing and local centre of gravity attraction (2013)
- Distance measures between digital fuzzy objects and their applicability in image processing (2011)
- Precise Estimation of the Projection of a Shape from a Pixel Coverage Representation (2011)
- The Sum of minimal distances as a useful distance measure for image registration (2010)
- De-noising of SRµCT Fiber Images by Total Variation Minimization (2010)
- Methods for 3D Visualization of Bone Tissue in the Proximity of Implants (2010)
- Methods for Visualization of Bone Tissue in the Proximity of Implants (2010)
- Estimation of linear deformations of 3D objects (2010)
- Spectral Angle Histogram (2009)
- Dimensionality Reduction for Colour Based Pixel Classification (2009)
- On set distances and their application to image registration (2009)
- Improved Quantification of Bone Remodelling by Utilizing Fuzzy Based Segmentation (2009)
- Sub-pixel Segmentation with the Image Foresting Transform (2009)
- Quantification of Bone Remodeling in SRuCTImages of Implants (2009)
- Pixel Coverage Segmentation for Improved Feature Estimation (2009)
- Recovering Affine Deformations of Fuzzy Shapes (2009)
- Algorithms for cross-talk suppression in fluorescence microscopy (2008)
- Non-uniform 3D distance transform for anisotropic signal correction in confocal image volumes of skeletal muscle cell nuclei (2008)
- Correction in 3D Confocal Images (2008)
- Deterministic Defuzzification based on Spectral Projected Gradient Optimization (2008)
- An Automated Image Analysis Method for Measuring Fibre Contact in Fibrous and Composite Materials (2008)
- Spatially-variant morphological operations on binary images based on the polar distance transform (2008)
- The polar distance transform (2008)
- Registration of 2D Histological Images of Bone Implants with 3D SRμCT Volumes (2008)
- Registration of 2D Histological Images of Bone Implants with 3D SRuCT Volumes (2008)
- Are all state of the art techniques "simple as that" to implement in biomaterials research? (2008)
- Att hitta ett histologiskt 2D snitt av ett benimplantat i en 3D mikrotomografivolym (2008)
- The spatial distribution of nuclei in single skeletal muscle cells as visualised by 3-D images: (2007)
- Analysis of Skeletal Fibers in Three Dimensional Images (2007)
- Analysis of Skeletal Fibers in Three Dimensional Images (2007)
- Defuzzification by Feature Distance Minimization Based on DC Programming (2007)
- Grey Weighted Polar Distance Transform for Outlining Circular and Approximately Circular Objects (2007)
- Quantification of bone remodeling in the proximity of implants (2007)
- Analysis of Histological Image and SRuCT Image Volumes of Bone Remodeling Around Implants (2007)
- Image Analysis of Bone Tissue Remodelling Around Implants (2007)
- Detailed quantification of the 3D structure of newsprints in X-ray synchrotron radiation microtomography images (2006)
- Stress transfer and failure in pulpfibre reinforced composites (2006)
- Feature Based Defuzzification at Increased Spatial Resolution (2006)
- Feature Based Defuzzification in Z² and Z³ Using a Scale Space Approach (2006)
- Damage Mechanisms in Paper (2006)
- Surface Volume Estimation of Digitized Hyperplanes Using Weighted Local Configurations (2005)
- Estimation of moments of digitized objects with fuzzy borders (2005)
- Segmentation and separation of point like fluorescent markers in digital images (2004)
- Segmentation of point-like fluorescent markers (2004)
- Defuzzification of discrete objects by optimizing area and perimeter similarity (2004)
- Surface area estimation of digitized planes using weighted local configurations (2003)
- Surface area estimation of digitized 3D objects using local computations (2002)
- Perimeter and Area Estimates for Digitized Objects (2001)
- A Comparison of Methods for Estimation of Intensity Non-Uniformities in 2D and 3D Microscope Images of Fluorescence Stained Cells (2001)
- Statistical quality control for segmentation of fluorescence labelled cells (2001)
- Analysis of cells using image data from sequential immunofluorescence staining experiments (2001)
- Multiple tissue antigen analysis by sequential immunofluorescence staining and multi-dimensional image analysis (2001)
- Histogram thresholding using kernel density estimates (2000)
- Automatic cytoplasm segmentation of fluorescence labelled cells (2000)
- Algorithms for cytoplasm segmentation of fluorescence labeled cells grown in micro-fabricated structures (1999)
Reports
