Related papers: CTransformer: Deep-transformer-based 3D cell membr…
The nematode Caenorhabditis elegans (C. elegans) is used as a model organism to better understand developmental biology and neurobiology. C. elegans features an invariant cell lineage, which has been catalogued and observed using…
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…
The timing of cell divisions in early embryos during the In-Vitro Fertilization (IVF) process is a key predictor of embryo viability. However, observing cell divisions in Time-Lapse Monitoring (TLM) is a time-consuming process and highly…
During developmental processes such as embryogenesis, how a group of cells fold into specific structures, is a central question in biology that defines how living organisms form. Establishing tissue-level morphology critically relies on how…
Tracking many cells in time-lapse 3D image sequences is an important challenging task of bioimage informatics. Motivated by a study of brain-wide 4D imaging of neural activity in C. elegans, we present a new method of multi-cell tracking.…
Transformers have made remarkable progress towards modeling long-range dependencies within the medical image analysis domain. However, current transformer-based models suffer from several disadvantages: (1) existing methods fail to capture…
The distribution and interactions of cellular organelles play a critical role in mediating cellular physiology and pathology. Large-scale electron microscopy enables visualization of organelle distribution and interactions at the tissue…
Studying cell morphology changes in time is critical to understanding cell migration mechanisms. In this work, we present a deep learning-based workflow to segment cancer cells embedded in 3D collagen matrices and imaged with phase-contrast…
Alzheimer's disease (AD) is a multifactorial neurodegenerative disorder characterized by progressive cognitive decline and widespread epigenetic dysregulation in the brain. DNA methylation, as a stable yet dynamic epigenetic modification,…
Advances in optical neuroimaging techniques now allow neural activity to be recorded with cellular resolution in awake and behaving animals. Brain motion in these recordings pose a unique challenge. The location of individual neurons must…
Deep phenotyping is an emerging conceptual paradigm and experimental approach that seeks to measure many aspects of phenotypes and link them to understand the underlying biology. Successful deep phenotyping has mostly been applied in…
Signal transduction and cell function are governed by the spatiotemporal organization of membrane-associated molecules. Despite significant advances in visualizing molecular distributions by 3D light microscopy, cell biologists still have…
Tracking cells in time-lapse videos is an essential technique for monitoring cell population dynamics at a single-cell level. Current methods for cell tracking are developed on videos with mostly single, constant signals and do not detect…
3D cell tracking in a living organism has a crucial role in live cell image analysis. Cell tracking in C. elegans has two difficulties. First, cell migration in a consecutive frame is large since they move their head during scanning.…
Investigating the cellular internalization pathways of single molecules or single nano-objects is important to understanding cell-matter interactions and to applications in drug delivery and discovery. Imaging and tracking the motion of…
How microorganisms respond to and interact with their environment can vary significantly from individual to individual, which can have important microbiological and ecological implications. However, most microscopy techniques can only…
Tracking all nuclei of an embryo in noisy and dense fluorescence microscopy data is a challenging task. We build upon a recent method for nuclei tracking that combines weakly-supervised learning from a small set of nuclei center point…
Epigenetic Tracking is a mathematical model of biological cells, originally conceived to study embryonic development. Computer simulations proved the capacity of the model to generate complex 3-dimensional cellular structures, and the…
Transfer learning has gained attention in medical image analysis due to limited annotated 3D medical datasets for training data-driven deep learning models in the real world. Existing 3D-based methods have transferred the pre-trained models…
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…