Related papers: Seeing Cells Clearly: Evaluating Machine Vision St…
We combine confocal imaging, microfluidics and image analysis to record 3D-images of cells in flow. This enables us to recover the full 3D representation of several hundred living cells per minute. Whereas 3D confocal imaging has thus far…
Current biological and medical research is aimed at obtaining a detailed spatiotemporal map of a live cell's interior to describe and predict cell's physiological state. We present here an algorithm for complete 3-D modelling of cellular…
Background Analyzing images to accurately estimate the number of different cell types in the brain using automatic methods is a major objective in neuroscience. The automatic and selective detection and segmentation of neurons would be an…
Microscopy imaging techniques are instrumental for characterization and analysis of biological structures. As these techniques typically render 3D visualization of cells by stacking 2D projections, issues such as out-of-plane excitation and…
The shape of a cell contains essential information about its function within the biological system. Segmenting these structures from large-scale 3D microscopy images is challenging, limiting clinical insights especially for microglia,…
Although cell shape can reflect the mechanical and biochemical properties of the cell and its environment, quantification of 3D cell shapes within 3D tissues remains difficult, typically requiring digital reconstruction from a stack of 2D…
Cell segmentation in microscopy is a challenging problem, since cells are often asymmetric and densely packed. This becomes particularly challenging for extremely large images, since manual intervention and processing time can make…
We report on the 3-dimensional imaging of biological cells including living neurons by a recently developed fibered interferometric Scanning Optical Microscope. The topography and surface structure of mouse fibroblasts and hippocampal…
We present an in-depth investigation of a fully automated Fourier-based analysis to determine the cell size and the width of its distribution in 3D biological tissues. The results are thoroughly tested using generated images, and we offer…
Imaging dynamics of cellular morphogenesis with high spatial-temporal resolution in 3D is challenging, due to the low spatial resolution along the optical axis and photo-toxicity. However, some cellular structures are planar and hence 2D…
We present a scalable method for brain cell identification in multiview confocal light sheet microscopy images. Our algorithmic pipeline includes a hierarchical registration approach and a novel multiview version of semantic deconvolution…
We consider the problem of accurately identifying cell boundaries and labeling individual cells in confocal microscopy images, specifically, 3D image stacks of cells with tagged cell membranes. Precise identification of cell boundaries,…
Recent studies suggest a potential link between the physical structure of mitochondria and neurodegenerative diseases. With advances in Electron Microscopy techniques, it has become possible to visualize the boundary and internal membrane…
Segmentation, or the outlining of objects within images, is a critical step in the measurement and analysis of cells within microscopy images. While improvements continue to be made in tools that rely on classical methods for segmentation,…
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…
Modeling the 3D structures of cells and tissues is crucial in biology. Sequential cross-sectional images from electron microscopy provide high-resolution intracellular structure information. The segmentation of complex cell structures…
Cell detection in microscopy images is important to study how cells move and interact with their environment. Most recent deep learning-based methods for cell detection use convolutional neural networks (CNNs). However, inspired by the…
Biological cells, by definition, are the basic units which contain the fundamental molecules of life of which all living things are composed. Understanding how they function and differentiating cells from one another therefore is of…
In many tissues, cell type varies over single-cell length-scales, creating detailed spatial heterogeneities fundamental to physiological function. To gain understanding of this relationship between tissue function and detailed structure,…
Epithelial cells form diverse structures from squamous spherical organoids to densely packed pseudostratified tissues. Quantification of cellular properties in these contexts requires high-resolution deep imaging and computational…