相关论文: Automated three-dimensional single cell phenotypin…

Cell tracking is an essential tool in live-cell imaging to determine single-cell features, such as division patterns or elongation rates. Unlike in common multiple object tracking, in microbial live-cell experiments cells are growing,…

In Part I of this article we have developed a novel mechanobiological model of a Tissue Engineering process that accounts for the mechanisms through which an isotropic or anisotropic adherence condition regulates the active functions of the…

The precise characterization of plant morphology provides valuable insights into plant environment interactions and genetic evolution. A key technology for extracting this information is 3D segmentation, which delineates individual plant…

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…

We fully generalize a previously-developed computational geometry tool [1] to perform large-scale simulations of arbitrary two-dimensional faceted surfaces $z = h(x,y)$. Our method uses a three-component facet/edge/junction storage model,…

U-Net and its variants have been demonstrated to work sufficiently well in biological cell tracking and segmentation. However, these methods still suffer in the presence of complex processes such as collision of cells, mitosis and…

Cell shape has long been used to discern cell phenotypes and states, but the underlying premise has not been quantitatively tested. Here, we show that a single cell image can be used to discriminate its migration behavior by analyzing a…

Cell tracking and segmentation assist biologists in extracting insights from large-scale microscopy time-lapse data. Driven by local accuracy metrics, current tracking approaches often suffer from a lack of long-term consistency and the…

The alignment of fibers and cells in living tissues affect their mechanical properties and functionality. In this context, one can draw an analogy between tissues and nematic liquid crystal elastomers. We explore this analogy by growing…

In this paper we propose a workflow to detect and track mitotic cells in time-lapse microscopy image sequences. In order to avoid the requirement for cell lines expressing fluorescent markers and the associated phototoxicity, phase contrast…

Intracellular protein patterns regulate many vital cellular functions, such as the processing of spatiotemporal information or the control of shape deformations. To do so, pattern-forming systems can be sensitive to the cell geometry by…

We propose a 3D convolutional neural network to simultaneously segment and detect cell nuclei in confocal microscopy images. Mirroring the co-dependency of these tasks, our proposed model consists of two serial components: the first part…

Biomembranes play a central role in various phenomena like locomotion of cells, cell-cell interactions, packaging of nutrients, and in maintaining organelle morphology and functionality. During these processes, the membranes undergo…

Studying the growth and metabolism of microbes provides critical insights into their evolutionary adaptations to harsh environments, which are essential for microbial research and biotechnology applications. In this study, we developed an…

Thin leaves, fine stems, self-occlusion, non-rigid and slowly changing structures make plants difficult for three-dimensional (3D) scanning and reconstruction -- two critical steps in automated visual phenotyping. Many current solutions…

Multicellular systems play a key role in bioprocess and biomedical engineering. Cell ensembles encountered in these setups show phenotypic variability like size and biochemical composition. As this variability may result in undesired…

Segmentation is often an essential intermediate step in image analysis. A volume segmentation characterizes the underlying volume image in terms of geometric information--segments, faces between segments, curves in which several faces…

Nowadays, there are many approaches to acquire three-dimensional (3D) point clouds of maize plants. However, automatic stem-leaf segmentation of maize shoots from three-dimensional (3D) point clouds remains challenging, especially for new…

An optimization-based strategy is proposed for coupling three-dimensional and one-dimensional problems (3D-1D coupling) in the context of soil-root interaction simulations. This strategy, originally designed to tackle generic 3D-1D coupled…

For over two decades, image-based profiling has revolutionized cell phenotype analysis. Image-based profiling processes rich, high-throughput, microscopy data into thousands of unbiased measurements that reveal phenotypic patterns powerful…