Natasa Sladoje

Short presentation

Keywords

• algorithm development
• artificial intelligence
• biomedical image analysis
• deep learning
• discrete geometry
• image analysis
• image processing
• image registration
• information and communication technology (ict)
• medical image analysis
• pattern recognition

Research

Publications

Recent publications

• Investigating the Relevance of Contextual Information Towards Improving Deep CNN Based Oral Cancer Screening on Whole Slide Cytology Samples (2023)
• Automated detection, segmentation and measurement of major vessels and the trachea in CT pulmonary angiography (2023)
• Multimodal deformable image registration using contrastive learning of equivariant image representations (2023)
• Contrastive Learning of Equivariant Image Representations for Multimodal Deformable Registration (2023)
• Partial dimensional collapse in contrastive learning when using intermediate layers (2023)

All publications

Articles

• Automated detection, segmentation and measurement of major vessels and the trachea in CT pulmonary angiography (2023)
• INSPIRE (2023)
• Cross-Modality Sub-Image Retrieval using Contrastive Multimodal Image Representations (2022)
• Is image-to-image translation the panacea for multimodal image registration? (2022)
• Fast computation of mutual information in the frequency domain with applications to global multimodal image alignment (2022)
• Is Image-to-Image Translation the Panacea for Multimodal Image Registration? A Comparative Study (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)
• HISTOBREAST (2020)
• BIAFLOWS (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)
• An Objective Scoring Framework for Histology Slide Image Mosaics Applicable for the Reliable Benchmarking of Image Quality Assessment Algorithms (2018)
• 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)
• 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)
• Defuzzification of spatial fuzzy sets by feature distance minimization (2011)
• High-precision boundary length estimation by utilizing gray-level information (2009)
• Representation and Reconstruction of Fuzzy Disks by Moments (2007)
• Shape signaturs of fuzzy star-shaped sets based on distance from the centroid (2005)
• Measurements of digitized objects with fuzzy borders in 2D and 3D (2005)
• Efficiency of Characterizing Ellipses and Ellipsoids by Discrete Moments (2000)
• BIAFLOWS: A collaborative framework to benchmark bioimage analysis workflows
• Can representation learning for multimodal image registration be improved by supervision of intermediate layers?

Books

• Bioimage Data Analysis Workflows ‒ Advanced Components and Methods (2022)
• Discrete Geometry and Mathematical Morphology (2021)
• Combinatorial Image Analysis - (2020)
• Bioimage Data Analysis Workflows (2019)

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)

Conferences

• 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)
• Partial dimensional collapse in contrastive learning when using intermediate layers (2023)
• Can Representation Learning for Multimodal Image Registration be Improved by Supervision of Intermediate Layers? (2023)
• End-to-end Multiple Instance Learning with Gradient Accumulation (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)
• 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)
• Registration of Multimodal Microscopy Images using CoMIR – learned structural image representations (2021)
• Comir: Contrastive multimodal image representation for registration (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)
• Robust Symmetric Affine Image Registration (2019)
• Stochastic Distance Functions with Applications in Object Detection and Image Segmentation (2019)
• Stochastic Distance Transform (2019)
• Denoising of short exposure transmission electron microscopy images for ultrastructural enhancement (2018)
• Denoising of Short Exposure Transmission Electron Microscopy Images using CNN (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)
• 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)
• Estimation of linear deformations of 3D objects (2010)
• On set distances and their application to image registration (2009)
• Improved Quantification of Bone Remodelling by Utilizing Fuzzy Based Segmentation (2009)
• Pixel Coverage Segmentation for Improved Feature Estimation (2009)
• Recovering Affine Deformations of Fuzzy Shapes (2009)
• Deterministic Defuzzification based on Spectral Projected Gradient Optimization (2008)
• Defuzzification by Feature Distance Minimization Based on DC Programming (2007)
• Feature Based Defuzzification at Increased Spatial Resolution (2006)
• Feature Based Defuzzification in Z² and Z³ Using a Scale Space Approach (2006)
• Estimation of moments of digitized objects with fuzzy borders (2005)
• Defuzzification of discrete objects by optimizing area and perimeter similarity (2004)
• Perimeter and Area Estimations of Digitized Objects with Fuzzy Borders (2003)
• Measuring perimeter and area in low resolution images using a fuzzy approach (2003)
• Shape Description of Fuzzy Segmented Objects: Area and Perimeter Estimators (2003)
• The Reconstruction of the Digital Hyperbola Segment from Its Code (2000)
• Ellipses estimation from their digitization (1997)
• A characterization of digital disks by discrete moments (1997)

Reports

• Perimeter estimation based on grey level object representation (2008)
• Review of scientific papers on fuzzy shape analysis (2005)
• A Brief Review on Benno Artman's "Euclid - The Creation of Mathematics" (2005)
• Reviews on Scientific Papers on Application of Fuzzy Set Theory in Image Segmentation (2002)
• A report on 10th Summer School on Image Processing (2002)

Other

• The NEUBIAS Gateway (2020)