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High-throughput screening using cell images is an efficient method for screening new candidates for pharmaceutical drugs. To complete the screening process, it is essential to have an efficient process for analyzing cell images. This paper…
The processes taking place inside the living cell are now understood to the point where predictive computational models can be used to gain detailed understanding of important biological phenomena. A key challenge is to extrapolate this…
Single-cell trajectory analysis aims to reconstruct the biological developmental processes of cells as they evolve over time, leveraging temporal correlations in gene expression. During cellular development, gene expression patterns…
Determining cell identities in imaging sequences is an important yet challenging task. The conventional method for cell identification is via cell tracking, which is complex and can be time-consuming. In this study, we propose an innovative…
Self-organisation of individuals within large collectives occurs throughout biology. Mathematical models can help elucidate the individual-level mechanisms behind these dynamics, but analytical tractability often comes at the cost of…
Conventional multi-stage cell tracking approaches rely heavily on detection or segmentation in each frame as a prerequisite, requiring substantial resources for high-quality segmentation masks and increasing the overall prediction time. To…
In the past decades, advances in microscopy have made it possible to study the dynamics of individual biomolecules in vitro and resolve intramolecular kinetics that would otherwise be hidden in ensemble averages. More recently,…
We present a domain adaptation of video diffusion models to generate highly realistic time-lapse microscopy videos of cell division in HeLa cells. Although state-of-the-art generative video models have advanced significantly for natural…
Lineage tracing, the tracking of living cells as they move and divide, is a central problem in biological image analysis. Solutions, called lineage forests, are key to understanding how the structure of multicellular organisms emerges. We…
Cell competition is a quality control mechanism in tissues that results in the elimination of less fit cells. Over the past decade, the phenomenon of cell competition has been identified in many physiological and pathological contexts,…
Swarming or collective motion of living entities is one of the most common and spectacular manifestations of living systems having been extensively studied in recent years. A number of general principles have been established. The…
Cellular populations are typically heterogenous collections of cells at different points in their respective cell cycles, each with a cell cycle time that varies from individual to individual. As a result, true single-cell behavior,…
In multicellular organisms, cells coordinate their activities through cell-cell communication (CCC), which is crucial for development, tissue homeostasis, and disease progression. Recent advances in single-cell and spatial omics…
Quorum sensing is a decentralized biological process, through which a community of cells with no global awareness coordinate their functional behaviors based solely on cell-medium interactions and local decisions. This paper draws…
The biomedical imaging world is notorious for working with small amounts of data, frustrating state-of-the-art efforts in the computer vision and deep learning worlds. With large datasets, it is easier to make progress we have seen from the…
We study the problem of multi-target tracking and data association in video. We formulate this in terms of selecting a subset of high-quality tracks subject to the constraint that no pair of selected tracks is associated with a common…
Modelling, analysing and inferring triggering mechanisms in population reproduction is fundamental in many biological applications. It is also an active and growing research domain in mathematical biology. In this chapter, we review the…
Cells count become a challenging problem when the cells move in a continuous stream, and their boundaries are difficult for visual detection. To resolve this problem we modified the training and decision making processes using curriculum…
3D fluorescence microscopy of living organisms has increasingly become an essential and powerful tool in biomedical research and diagnosis. An exploding amount of imaging data has been collected, whereas efficient and effective…
The motion of a eukaryotic cell presents a variety of interesting and challenging problems from both a modeling and a computational perspective. The processes span many spatial scales (from molecular to tissue) as well as disparate time…