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Cell nuclei segmentation is one of the most important tasks in the analysis of biomedical images. With ever-growing sizes and amounts of three-dimensional images to be processed, there is a need for better and faster segmentation methods.…
Computer-aided analysis of biological microscopy data has seen a massive improvement with the utilization of general-purpose deep learning techniques. Yet, in microscopy studies of multi-organism systems, the problem of collision and…
The kinetics of the assembly of semiflexible filaments through end-to-end annealing is key to the structure of the cytoskeleton, but is not understood. We analyze this problem through scaling theory and simulations, and uncover a regime…
Objective: Modelling the associations from high-throughput experimental molecular data has provided unprecedented insights into biological pathways and signalling mechanisms. Graphical models and networks have especially proven to be useful…
Cryo-electron tomography (cryo-ET) is an emerging technology for the 3D visualization of structural organizations and interactions of subcellular components at near-native state and sub-molecular resolution. Tomograms captured by cryo-ET…
Segmenting cytoskeletal filaments in microscopy images is essential for studying their roles in cellular processes. However, this task is highly challenging due to the fine, densely packed, and intertwined nature of these structures.…
We investigate the mechanical interplay between the spatial organization of the actin cytoskeleton and the shape of animal cells adhering on micropillar arrays. Using a combination of analytical work, computer simulations and in vitro…
Quantitative analysis of the dynamics of tiny cellular and sub-cellular structures, known as particles, in time-lapse cell microscopy sequences requires the development of a reliable multi-target tracking method capable of tracking numerous…
The emerging field of connectomics aims to unlock the mysteries of the brain by understanding the connectivity between neurons. To map this connectivity, we acquire thousands of electron microscopy (EM) images with nanometer-scale…
The detection of cell shape changes in 3D time-lapse images of complex tissues is an important task. However, it is a challenging and tedious task to establish a comprehensive dataset to improve the performance of deep learning models. In…
Epigenetic Tracking (ET) is an Artificial Embryology system which allows for the evolution and development of large complex structures built from artificial cells. In terms of the number of cells, the complexity of the bodies generated with…
Single-particle electron cryomicroscopy (cryo-EM) is an increasingly popular technique for elucidating the three-dimensional structure of proteins and other biologically significant complexes at near-atomic resolution. It is an imaging…
We study image segmentation in the biological domain, particularly trait segmentation from specimen images (e.g., butterfly wing stripes, beetle elytra). This fine-grained task is crucial for understanding the biology of organisms, but it…
Curvilinear structures, which include line-like continuous objects, are fundamental geometrical elements in image-based applications. Reconstructing these structures from images constitutes a pivotal research area in computer vision.…
The development of traction-force microscopy, in the past two decades, has created the unprecedented opportunity of performing direct mechanical measurements on living cells as they adhere or crawl on uniform or micro-patterned substrates.…
Many properties of commonly used materials are driven by their microstructure, which can be influenced by the composition and manufacturing processes. To optimise future materials, understanding the microstructure is critically important.…
Knowledge of a protein's atomic conformational ensemble is critical to determining its function, yet state-of-the-art ensemble prediction models are limited by lack of high-quality conformational data from simulation or experiment. Recent…
Myosin motor proteins drive vigorous steady-state fluctuations in the actin cytoskeleton of cells. Endogenous embedded semiflexible filaments such as microtubules, or added filaments such as single-walled carbon nanotubes are used as novel…
Cellular electron cryo-tomography enables the 3D visualization of cellular organization in the near-native state and at submolecular resolution. However, the contents of cellular tomograms are often complex, making it difficult to…
Automatic segmentation of abdomen organs using medical imaging has many potential applications in clinical workflows. Recently, the state-of-the-art performance for organ segmentation has been achieved by deep learning models, i.e.,…