Related papers: Reconstruction of the 3D structure and development…
Wire-Cell is a 3D event reconstruction package for liquid argon time projection chambers. Through geometry, time, and drifted charge from multiple readout wire planes, 3D space points with associated charge are reconstructed prior to the…
Cell lineage decisions occur in three-dimensional spatial patterns that are difficult to identify by eye. There is an ongoing effort to replicate such patterns using mathematical modeling. One approach uses long ranging cell-cell…
This article considers the problem of 3-dimensional genome reconstruction for single-cell data, and the uniqueness of such reconstructions in the setting of haploid organisms. We consider multiple graph models as representations of this…
A software for processing sets of full-color images of biological tissue histological sections is developed. We used histological sections obtained by the method of high-precision layer-by-layer grinding of frozen biological tissues. The…
Automated sample preparation and electron microscopy enables acquisition of very large image data sets. These technical advances are of special importance to the field of neuroanatomy, as 3D reconstructions of neuronal processes at the nm…
CRISPR technology has enabled large-scale cell lineage tracing for complex multicellular organisms by mutating synthetic genomic barcodes during organismal development. However, these sophisticated biological tools currently use ad-hoc and…
We present a method for recovering the structure of a plant directly from a small set of widely-spaced images. Structure recovery is more complex than shape estimation, but the resulting structure estimate is more closely related to…
Neurological diseases and injuries present some of the greatest challenges in modern medicine, often causing irreversible and lifelong burdens in the people whom they afflict. These diagnoses have devastating consequences on millions of…
The measurement of cellular traction forces on soft elastic substrates has become a standard tool for many labs working on mechanobiology. Here we review the basic principles and different variants of this approach. In general, the…
Highly multiplexed microscopy enables rich spatial characterization of tissues at single-cell resolution, yet most analyses rely on two-dimensional sections despite inherently three-dimensional tissue organization. Acquiring dense…
Lineage tracing, the determination and mapping of progeny arising from single cells, is an important approach enabling the elucidation of mechanisms underlying diverse biological processes ranging from development to disease. We developed a…
A method is proposed for high-resolution, three-dimensional reconstruction of internal structure of objects from planar transmission images. The described approach can be used with any form of radiation or matter waves, in principle,…
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…
In man-made environments such as indoor scenes, when point-based 3D reconstruction fails due to the lack of texture, lines can still be detected and used to support surfaces. We present a novel method for watertight piecewise-planar surface…
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,…
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…
Accurate reconstruction of leaf surfaces from 3D point cloud is essential for agricultural applications such as phenotyping. However, real-world plant data (i.e., irregular 3D point cloud) are often complex to reconstruct plant parts…
Over the last two decades, scientific literature has been blooming with various means of simulating epithelial cell colonies. Each of these simulations can be separated by their respective efficiency (expressed in terms of consumed…
Modern technology for producing extremely bright and coherent X-ray laser pulses provides the possibility to acquire a large number of diffraction patterns from individual biological nanoparticles, including proteins, viruses, and DNA.…
Cell segmentation and tracking allow us to extract a plethora of cell attributes from bacterial time-lapse cell movies, thus promoting computational modeling and simulation of biological processes down to the single-cell level. However, to…