Related papers: Single cell resolution 3D imaging and segmentation…
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…
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,…
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,…
Current in vivo microscopy allows us detailed spatiotemporal imaging (3D+t) of complete organisms and offers insights into their development on the cellular level. Even though the imaging speed and quality is steadily improving,…
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…
Data-driven cell tracking and segmentation methods in biomedical imaging require diverse and information-rich training data. In cases where the number of training samples is limited, synthetic computer-generated data sets can be used to…
Biological cell imaging has become one of the most crucial research interests due to its wide-ranging applications in biomedical and microbiology studies. However, three-dimensional (3D) imaging of biological cells remains critically…
Volume electron microscopy is the method of choice for the in-situ interrogation of cellular ultrastructure at the nanometer scale. Recent technical advances have led to a rapid increase in large raw image datasets that require…
While high-resolution microscopic techniques are crucial for studying cellular structures in cell biology, obtaining such images from thick 3D engineered tissues remains challenging. In this review, we explore advancements in fluorescence…
Tracking of plant cells in images obtained by microscope is a challenging problem due to biological phenomena such as large number of cells, non-uniform growth of different layers of the tightly packed plant cells and cell division.…
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…
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…
Modern spatial microscopy has provided developmental biology with powerful research tools. However, the recent significant technological breakthroughs have inevitably led to technical "bottlenecks" for the application of the new procedures…
A method is presented to quantify resolution as a function of depth in features of morphologically complex 3D samples. Applying the method to the brain of Drosophila, resolution is measured at increasing depth throughout the central brain…
The maintenance of tissue and organ structures during dynamic homeostasis is often not well understood. In order for a system to be stable, cell renewal, cell migration and cell death must be finely balanced. Moreover, a tissue's shape must…
Advances in fluorescence microscopy enable acquisition of 3D image volumes with better image quality and deeper penetration into tissue. Segmentation is a required step to characterize and analyze biological structures in the images and…
The spread of microbial infections is governed by the self-organization of bacteria on surfaces. Limitations of live imaging techniques make collective behaviors in clinically relevant systems challenging to quantify. Here, novel…
This paper presents a method for time-lapse 3D cell analysis. Specifically, we consider the problem of accurately localizing and quantitatively analyzing sub-cellular features, and for tracking individual cells from time-lapse 3D confocal…
In this article, we propose a general framework to study the dynamics and topology of cellular networks that capture the geometry of cell packings in two-dimensional tissues. Such epithelia undergo large-scale deformation during…
Numerical investigation of the interaction of electromagnetic fields with eukaryotic cells requires specifically adapted computer models. Virtual microdosimetry, used to investigate exposure, requires volumetric cell models, which are…