Cube 20th projector central8/18/2023 ![]() Adjusting imaging parameters and views of these images made it possible to study features of larger-scale structures, such as the gills and the gut, that are normally inaccessible to histology. created three-dimensional images of whole zebrafish, measuring three millimeters to about a centimeter in length. To test their modified CT system, Ding et al. have developed a new method, by optimizing multiple components of CT scanning, that begins to provide the higher resolution and contrast needed to make diagnoses that require histological detail. ![]() However, the resolution (the ability to distinguish between objects) and tissue contrast of these images has been insufficient for histology-based diagnosis across all cell types. This technique has also been applied to image smaller structures. Larger internal structures within the human body are routinely visualized using a technique known as computerized tomography, CT for short – whereby dozens of x-ray images are compiled together to generate a three-dimensional image. Histology’s dependence upon such thin slices makes it impossible to see the entirety of cells and structures that are thicker than the slice, or to accurately measure three-dimensional features such as shape or volume. To allow individual cells to be distinguished, tissues are cut into slices less than 1/20th of a millimeter thick. But despite its frequent use, histology comes with limitations. This powerful technique has revolutionized biology and medicine. A common way of studying these microscopic cell changes is by an approach called histology: thin slices of centimeter-sized samples of tissues are taken from patients, stained to distinguish cellular components, and examined for abnormal features. We expect the computational and visual insights into 3D cell and tissue architecture provided by histotomography to be useful for reference atlases, hypothesis generation, comprehensive organismal screens, and diagnostics.ĭiagnosing diseases, such as cancer, requires scientists and doctors to understand how cells respond to different medical conditions. Unlike histology, the histotomography also allows the study of 3-dimensional structures of millimeter scale that cross multiple tissue planes. Striking individual phenotypic variation was apparent from color maps of computed densities of brain nuclei. Micro-CT optimized for cellular characterization (histotomography) allows brain nuclei to be computationally segmented and assigned to brain regions, and cell shapes and volumes to be computed for motor neurons and red blood cells. To determine how synchrotron-based X-ray micro-tomography (micro-CT) can yield 3-dimensional whole-organism images suitable for quantitative histological phenotyping, we scanned whole zebrafish, a small vertebrate model with diverse tissues, at ~1 micron voxel resolutions. Histology is a powerful way to detect cellular and tissue phenotypes, but is largely descriptive and subjective. Organismal phenotypes frequently involve multiple organ systems. ViBE-Z: A Framework for 3D Virtual Colocalization Analysis in Zebrafish Larval Brains. Ronneberger O, Liu K, Rath M, Rueß D, Mueller T, Skibbe H, Drayer B, Schmidt T, Filippi A, Nitschke R, Brox T, Burkhardt H, Driever W. The following previously published dataset was used: Data from: Computational 3D histological phenotyping of whole zebrafish by X-ray histotomography. Due to the large size of these files, use of a traditional repository at the time of publication was impractical.ĭing Y, Vanselow D, Yakovlev M, Katz S, Lin A, Clark D, Vargas P, Xin X, Copper J, Canfield V, Ang K, Wang Y, Xiao X, Carlo FD, Rossum Dv, Riviere PL, Cheng K. Full bit-depth scans, including raw projection data, are available from researchers upon request as a download or transfer to physical media. Registered and unregistered 8-bit reconstructions of the heads of five zebrafish larvae involved in analysis are available on Dryad ( ) along with scripts written for cell nuclei detection, analysis, and sample registration. Digital histology is publicly available from our Zebrafish Lifespan Atlas ( ) (Cheng, 2004).
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