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Cell segmentation is a critical step for quantitative single-cell analysis in microscopy images. Existing cell segmentation methods are often tailored to specific modalities or require manual interventions to specify hyper-parameters in…
Diagnosing diseases such as leukemia or anemia requires reliable counts of blood cells. Hematologists usually label and count microscopy images of blood cells manually. In many cases, however, cells in different maturity states are…
Cell biologists study in parallel the morphology of cells with the regulation mechanisms that modify this morphology. Such studies are complicated by the inherent heterogeneity present in the cell population. It remains difficult to define…
Representation learning has driven major advances in natural image analysis by enabling models to acquire high-level semantic features. In microscopy imaging, however, it remains unclear what current representation learning methods actually…
This report presents a generic image registration benchmark with automatic evaluation using landmark annotations. The key features of the BIRL framework are: easily extendable, performance evaluation, parallel experimentation, simple…
Living systems, particularly multicellular systems, often seem hopelessly complex. But recent studies have suggested that beneath this complexity, there may be unifying quantitative principles that we are only now starting to unravel. All…
This article presents formalistic tool for description of structural and biochemical relations between cells in the course of development of the body of plants. This is flexible formalistic space, based on the Category theory and the Petri…
The demand of transparency of clinical research results, the need of accelerating the process of transferring innovation in the daily medical practice as well as assuring patient safety and product efficacy make it necessary to extend the…
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…
The two pillars of Algebraic topology - Homology and homotopy theory rely on the availability of basic building blocks called cells. Cells take the form of simplexes, and have properties such as faces, sub-cells, convexity and…
Single-cell RNA sequencing (scRNA-seq) enables the study of cellular diversity at single cell level. It provides a global view of cell-type specification during the onset of biological mechanisms such as developmental processes and human…
Determining the trajectories of cells and their lineages or ancestries in live-cell experiments are fundamental to the understanding of how cells behave and divide. This paper proposes novel online algorithms for jointly tracking and…
The organization of cells within tissues plays a vital role in various biological processes, including development and morphogenesis. As a result, understanding how cells self-organize in tissues has been an active area of research. In our…
Single-cell RNA-seq (scRNA-seq) enables atlas-scale profiling of complex tissues, revealing rare lineages and transient states. Yet, assigning biologically valid cell identities remains a bottleneck because markers are tissue- and…
Modern single-cell flow and mass cytometry technologies measure the expression of several proteins of the individual cells within a blood or tissue sample. Each profiled biological sample is thus represented by a set of hundreds of…
Metacells are disjoint and homogeneous groups of single-cell profiles, representing discrete and highly granular cell states. Existing metacell algorithms tend to use only one modality to infer metacells, even though single-cell multi-omics…
Microscopy imaging plays a vital role in understanding many biological processes in development and disease. The recent advances in automation of microscopes and development of methods and markers for live cell imaging has led to rapid…
Machine learning (ML) methods are proliferating in scientific research. However, the adoption of these methods has been accompanied by failures of validity, reproducibility, and generalizability. These failures can hinder scientific…
Understanding the mechanisms of interactions within cells, tissues, and organisms is crucial to driving developments across biology and medicine. Mathematical modeling is an essential tool for simulating biological systems and revealing…
Entity linking (EL) is the task of linking a textual mention to its corresponding entry in a knowledge base, and is critical for many knowledge-intensive NLP applications. When applied to tables in scientific papers, EL is a step toward…