scholarly journals 3D visualization of macromolecule synthesis

eLife ◽  
2020 ◽  
Vol 9 ◽  
Author(s):  
Timothy J Duerr ◽  
Ester Comellas ◽  
Eun Kyung Jeon ◽  
Johanna E Farkas ◽  
Marylou Joetzjer ◽  
...  
Keyword(s):  
3D Visualization ◽  
Fluorescent Microscopy ◽  
Three Dimensional ◽  
Light Sheet ◽  
Macromolecular Synthesis ◽  
Volumetric Imaging ◽  
Processing Pipeline ◽  
Powerful Means

Measuring nascent macromolecular synthesis in vivo is key to understanding how cells and tissues progress through development and respond to external cues. Here we perform in vivo injection of alkyne- or azide-modified analogs of thymidine, uridine, methionine, and glucosamine to label nascent synthesis of DNA, RNA, protein, and glycosylation. Three-dimensional volumetric imaging of nascent macromolecule synthesis was performed in axolotl salamander tissue using whole-mount click chemistry-based fluorescent staining followed by light sheet fluorescent microscopy. We also developed an image processing pipeline for segmentation and classification of morphological regions of interest and individual cells, and we apply this pipeline to the regenerating humerus. We demonstrate our approach is sensitive to biological perturbations by measuring changes in DNA synthesis after limb denervation. This method provides a powerful means to quantitatively interrogate macromolecule synthesis in heterogenous tissues at the organ, cellular, and molecular levels of organization.

scholarly journals 3D Visualization of Macromolecule Synthesis

2020 ◽  
Author(s):  
Timothy J. Duerr ◽  
Ester Comellas ◽  
Eun Kyung Jeon ◽  
Johanna E. Farkas ◽  
Marylou Joetzjer ◽  
...  
Keyword(s):  
3D Visualization ◽  
Fluorescent Microscopy ◽  
Three Dimensional ◽  
Light Sheet ◽  
Macromolecular Synthesis ◽  
Volumetric Imaging ◽  
Processing Pipeline ◽  
Powerful Means

AbstractMeasuring nascent macromolecular synthesis in vivo is key to understanding how cells and tissues progress through development and respond to external cues. Here, we perform in vivo injection of alkyne- or azide-modified analogs of thymidine, uridine, methionine, and glucosamine to label nascent synthesis of DNA, RNA, protein, and glycosylation. Three-dimensional volumetric imaging of nascent macromolecule synthesis was performed in axolotl salamander tissue using whole mount click chemistry-based fluorescent staining followed by light sheet fluorescent microscopy. We also developed an image processing pipeline for segmentation and classification of morphological regions of interest and individual cells, and we apply this pipeline to the regenerating humerus. We demonstrate our approach is sensitive to biological perturbations by measuring changes in DNA synthesis after limb denervation. This method provides a powerful means to quantitatively interrogate macromolecule synthesis in heterogenous tissues at the organ, cellular, and molecular levels of organization.

scholarly journals Light Sheet Microscopy-Assisted 3D Analysis of SARS-CoV-2 Infection in the Respiratory Tract of the Ferret Model

Viruses ◽  
2021 ◽  
Vol 13 (3) ◽  
pp. 529
Author(s):  
Luca M. Zaeck ◽  
David Scheibner ◽  
Julia Sehl ◽  
Martin Müller ◽  
Donata Hoffmann ◽  
...  
Keyword(s):  
Respiratory Tract ◽  
3D Visualization ◽  
Three Dimensional ◽  
Light Sheet ◽  
3D Analysis ◽  
Respiratory Pathogens ◽  
Upper Respiratory Tract ◽  
Thin Sections ◽  
Light Sheet Microscopy

The visualization of viral pathogens in infected tissues is an invaluable tool to understand spatial virus distribution, localization, and cell tropism in vivo. Commonly, virus-infected tissues are analyzed using conventional immunohistochemistry in paraffin-embedded thin sections. Here, we demonstrate the utility of volumetric three-dimensional (3D) immunofluorescence imaging using tissue optical clearing and light sheet microscopy to investigate host–pathogen interactions of pandemic SARS-CoV-2 in ferrets at a mesoscopic scale. The superior spatial context of large, intact samples (>150 mm3) allowed detailed quantification of interrelated parameters like focus-to-focus distance or SARS-CoV-2-infected area, facilitating an in-depth description of SARS-CoV-2 infection foci. Accordingly, we could confirm a preferential infection of the ferret upper respiratory tract by SARS-CoV-2 and suggest clustering of infection foci in close proximity. Conclusively, we present a proof-of-concept study for investigating critically important respiratory pathogens in their spatial tissue morphology and demonstrate the first specific 3D visualization of SARS-CoV-2 infection.

scholarly journals Zebrafish Vascular Quantification (ZVQ): a tool for quantification of three-dimensional zebrafish cerebrovascular architecture by automated image analysis

Development ◽  
2022 ◽  
Author(s):  
E. C. Kugler ◽  
J. Frost ◽  
V. Silva ◽  
K. Plant ◽  
K. Chhabria ◽  
...  
Keyword(s):  
Image Analysis ◽  
Rapid Assessment ◽  
Three Dimensional ◽  
Vascular Anatomy ◽  
Light Sheet ◽  
Automated Image Analysis ◽  
Cerebral Vasculature ◽  
Experimental Conditions ◽  
Branching Points

Zebrafish transgenic lines and light sheet fluorescence microscopy allow in-depth insights into three-dimensional vascular development in vivo. However, quantification of the zebrafish cerebral vasculature in 3D remains highly challenging. Here, we describe and test an image analysis workflow for 3D quantification of the total or regional zebrafish brain vasculature, called zebrafish vasculature quantification “ZVQ”. It provides the first landmark- or object-based vascular inter-sample registration of the zebrafish cerebral vasculature, producing Population Average Maps allowing rapid assessment of intra- and inter-group vascular anatomy. ZVQ also extracts a range of quantitative vascular parameters from a user-specified Region of Interest including volume, surface area, density, branching points, length, radius, and complexity. Application of ZVQ to thirteen experimental conditions, including embryonic development, pharmacological manipulations and morpholino induced gene knockdown, shows ZVQ is robust, allows extraction of biologically relevant information and quantification of vascular alteration, and can provide novel insights into vascular biology. To allow dissemination, the code for quantification, a graphical user interface, and workflow documentation are provided. Together, ZVQ provides the first open-source quantitative approach to assess the 3D cerebrovascular architecture in zebrafish.

scholarly journals Multi-color 4D superresolution light-sheet microscopy reveals organelle interactions at isotropic 100-nm resolution and sub-second timescales

2021 ◽  
Author(s):  
Peng Fei
Keyword(s):  
Dimensional Space ◽  
Three Dimensional ◽  
Light Sheet ◽  
Three Dimensions ◽  
Live Cells ◽  
Spatiotemporal Resolution ◽  
Volumetric Imaging ◽  
Light Sheet Microscopy ◽  
Intracellular Organelles ◽  
Microscopy Techniques

Long-term visualization of the dynamic organelle-organelle or protein-organelle interactions throughout the three-dimensional space of whole live cells is essential to better understand their functions, but this task remains challenging due to the limitations of existing three-dimensional fluorescence microscopy techniques, such as an insufficient axial resolution, low volumetric imaging rate, and photobleaching. Here, we present the combination of a progressive deep-learning superresolution strategy with a dual-ring-modulated SPIM design capable of visualizing the dynamics of intracellular organelles in live cells for hours at an isotropic spatial resolution of ~100 nm in three dimensions and a temporal resolution up to ~17 Hz. With a compelling spatiotemporal resolution, we substantially reveal the complex spatial relationships and interactions between the endoplasmic reticulum (ER) and mitochondria throughout live cells, providing new insights into ER-mediated mitochondrial division. We also localized the motion of Drp1 oligomers in three dimensions and observed Drp1-mediated mitochondrial branching for the first time.

scholarly journals Three-dimensional, isotropic imaging of mouse brain using multi-view deconvolution light sheet microscopy

2017 ◽  
Vol 10 (05) ◽  
pp. 1743006 ◽  
Author(s):  
Sa Liu ◽  
Jun Nie ◽  
Yusha Li ◽  
Tingting Yu ◽  
Dan Zhu ◽  
...  
Keyword(s):  
Mouse Brain ◽  
Pyramidal Neurons ◽  
Structural Information ◽  
Fluorescent Microscopy ◽  
Three Dimensional ◽  
Light Sheet ◽  
Nerve Fibers ◽  
Single View ◽  
Light Sheet Microscopy ◽  
The Brain

We present a three-dimensional (3D) isotropic imaging of mouse brain using light-sheet fluorescent microscopy (LSFM) in conjunction with a multi-view imaging computation. Unlike common single view LSFM is used for mouse brain imaging, the brain tissue is 3D imaged under eight views in our study, by a home-built selective plane illumination microscopy (SPIM). An output image containing complete structural information as well as significantly improved resolution ([Formula: see text]4 times) are then computed based on these eight views of data, using a bead-guided multi-view registration and deconvolution. With superior imaging quality, the astrocyte and pyramidal neurons together with their subcellular nerve fibers can be clearly visualized and segmented. With further including other computational methods, this study can be potentially scaled up to map the connectome of whole mouse brain with a simple light-sheet microscope.

Clinical applications of three-dimensional magnetic resonance image analysis

1996 ◽  
Vol 86 (1) ◽  
pp. 33-37 ◽  
Author(s):  
GR Bauer ◽  
HJ Hillstrom ◽  
JK Udupa ◽  
BE Hirsch
Keyword(s):  
Magnetic Resonance ◽  
Surgical Planning ◽  
Three Dimensional ◽  
Magnetic Resonance Images ◽  
Application Development ◽  
Dimensional Reconstruction ◽  
Foot Function ◽  
Broad Clinical Application

A methodology for measuring the kinematic parameters of joints in vivo has been refined using the technique of computerized three-dimensional reconstruction from magnetic resonance images. A research protocol has been developed to establish a classification of normal and pathologic foot function that will have broad clinical application. Development of algorithms for a computer-directed program that can predict resultant kinematics and joint morphometry for a given osteotomy or osseous remodeling procedure will assist the surgeon in preoperative surgical planning.

3D Visualization of Maize Stem by MRI Technology

2001 ◽  
Vol 7 (S2) ◽  
pp. 100-101
Author(s):  
P. C. Cheng ◽  
J. H. Chen ◽  
S. C. Hwang ◽  
C. K. Sun ◽  
D. B. Walden ◽  
...  
Keyword(s):  
Soft Tissues ◽  
Sweet Corn ◽  
3D Visualization ◽  
Spin Echo ◽  
Three Dimensional ◽  
Slice Thickness ◽  
Volumetric Imaging ◽  
Dimensional Reconstruction ◽  
Inner Diameter ◽  
Imaging Artifact

Recent development in confocal and multi-photon microscopy allows 3D imaging of plant tissue in high resolution. However, other than physical sectioning, macroscopical study of plant organs in 3D remains a difficult task. Among various available technologies for macroscopical imaging (e.g., Xray macro-tomography, optical coherent tomography and MRI), MRI is an ideal choice for its contrasting modality in volumetric imaging of soft tissues. A 3T Biospect MRI system (Brucker, Germany)(FIG 1) equipped with a 6cm inner diameter micro-quadrature coil (FIG 2) for RF transmission and reception of MRI signals was used in this study. Spin echo based RARE sequence was used to obtain T2 weighted images with TR/TE = 3160.5/58.5ms and field-of-view of 1.67cm × 1.67cm (256 × 256 pixels) at a slice thickness of 0.8mm. This corresponds to a voxel size of 65 × 65 × 800μm. Data was obtained within 1/2 hour with number-of-excitations (nex) set at 16. Figure 4 (a-x) shows a series of MRI sections through a stem node (the node below the main ear insertion) from field-grown maize (Zea mays, van Odyssey sweet corn). The stem was fixed in 1:3 EtOH/acetic acid, washed thoroughly in water prior to imaging. Air bubbles trapped in the tissue were removed by vacuuming, to avoid imaging artifact due to low magnetic susceptibility of air. Figure 5 (a-g) shows reconstructed longitudinal sections. Three-dimensional reconstruction (FIG. 3) was performed by using Vaytek VoxBlast™ and AutoQuant’s AutoVisulize 3D™ software. in combination with image segmentation and tracing tools, the MRI technology will greatly enhance our capability in the understanding of vascular architecture and its development in plants.

scholarly journals 3D Visualization and Volume-Based Quantification of Rice Chalkiness In Vivo by Using High Resolution Micro-CT

Rice ◽  
2020 ◽  
Vol 13 (1) ◽  
Author(s):  
Yi Su ◽  
Lang-Tao Xiao
Keyword(s):  
High Throughput ◽  
High Throughput Screening ◽  
3D Visualization ◽  
Three Dimensional ◽  
Basic Research ◽  
Micro Ct ◽  
Milled Rice ◽  
Phenotype Analysis ◽  
Rice Seeds

Abstract Background Rice quality research attracts attention worldwide. Rice chalkiness is one of the key indexes determining rice kernel quality. The traditional rice chalkiness measurement methods only use milled rice as materials and are mainly based on naked-eye observation or area-based two-dimensional (2D) image analysis and the results could not represent the three-dimensional (3D) characteristics of chalkiness in the rice kernel. These methods are neither in vivo thus are unable to analyze living rice seeds for high throughput screening of rice chalkiness phenotype. Results Here, we introduced a novel method for 3D visualization and accurate volume-based quantification of rice chalkiness in vivo by using X-ray microcomputed tomography (micro-CT). This approach not only develops a novel volume-based method to measure the 3D rice chalkiness index, but also provides a high throughput solution for rice chalkiness phenotype analysis by using living rice seeds. Conclusions Our method could be a new powerful tool for rice chalkiness measurement, especially for high throughput chalkiness phenotype screening using living rice seeds. This method could be used in chalkiness phenotype identification and screening, and would greatly promote the basic research in rice chalkiness regulation as well as the quality evaluation in rice production practice.

scholarly journals Light-Sheet Microscopy in Neuroscience

2019 ◽  
Vol 42 (1) ◽  
pp. 295-313 ◽  
Author(s):  
Elizabeth M.C. Hillman ◽  
Venkatakaushik Voleti ◽  
Wenze Li ◽  
Hang Yu
Keyword(s):  
High Speed ◽  
Light Sheet ◽  
Mammalian Brain ◽  
Diverse Range ◽  
Volumetric Imaging ◽  
Two Photon Microscopy ◽  
Light Sheet Microscopy ◽  
Noise Benefits ◽  
Longitudinal Imaging

Light-sheet microscopy is an imaging approach that offers unique advantages for a diverse range of neuroscience applications. Unlike point-scanning techniques such as confocal and two-photon microscopy, light-sheet microscopes illuminate an entire plane of tissue, while imaging this plane onto a camera. Although early implementations of light sheet were optimized for longitudinal imaging of embryonic development in small specimens, emerging implementations are capable of capturing light-sheet images in freely moving, unconstrained specimens and even the intact in vivo mammalian brain. Meanwhile, the unique photobleaching and signal-to-noise benefits afforded by light-sheet microscopy's parallelized detection deliver the ability to perform volumetric imaging at much higher speeds than can be achieved using point scanning. This review describes the basic principles and evolution of light-sheet microscopy, followed by perspectives on emerging applications and opportunities for both imaging large, cleared, and expanded neural tissues and high-speed, functional imaging in vivo.

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