3d Confocal Microscopy
3d Confocal Microscopy - Related Videos
08:00
Correlative Confocal and 3D Electron Microscopy of a Specific Sensory Cell
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Cited by 7 •
2015
Here, we introduce a method, cocem3D, to unveil the ultrastructure of a specific cell in its native tissue by bridging confocal and serial block-face scanning electron microscopy.
10:48
Imaging Biological Samples with Optical and Confocal Microscopy
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2023
Source: Peiman Shahbeigi-Roodposhti and Sina Shahbazmohamadi, Biomedical Engineering Department, University of Connecticut, Storrs, Connecticut Optical microscopes have been around for centuries, and while they reached their theoretical limitation of resolution decades ago, new equipment and techniques, such as confocal and digital image processing, have created new niches within the field of optical imaging. The best optical microscopes will typically have a resolution down to 200 nm in ideal...
03:16
Three-dimensional Imaging of Immunolabeled Astrocytes Using Confocal Microscopy
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2025
Source: Bagheri, M., et. al. Protocol for Three-dimensional Confocal Morphometric Analysis of Astrocytes. J. Vis. Exp. (2015).This video demonstrates the imaging of fluorescently labeled astrocytes in a mouse brain section using a confocal microscope. The brain section is positioned under the appropriate objective lens, and suitable fluorophores and filters are selected. After optimizing the exposure automatically, the scanning parameters are defined to ensure high-resolution 2D images. Z-stack...
17:08
In vivo Clonal Tracking of Hematopoietic Stem and Progenitor Cells Marked by Five Fluorescent Proteins using Confocal and Multiphoton Microscopy
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Cited by 11 •
2014
Combinatorial 5 fluorescent proteins marking of hematopoietic stem and progenitor cells allows in vivo clonal tracking via confocal and two-photon microscopy, providing insights into bone marrow hematopoietic architecture during regeneration. This method allows non-invasive fate mapping of spectrally-coded HSPCs-derived cells in intact tissues for extensive periods of time following transplantation.
05:25
Quantification of Dendritic Spines Using Confocal Microscopy Imaging
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2025
Source: Gouder, et. al. Three-dimensional Quantification of Dendritic Spines from Pyramidal Neurons Derived from Human Induced Pluripotent Stem Cells. J. Vis. Exp. (2015).This video demonstrates the imaging and analysis of dendritic spines in transduced, immunolabeled pyramidal neurons using confocal microscopy. Background noise is reduced, and dendrites are traced by estimating their diameter and length. Automated spine segmentation involves setting parameters for dendrite and spine dimensions...
FAQs
The pinhole improves image contrast by rejecting light that originates away from the selected focal plane. During scanning, the focused laser interrogates one point at a time, and the recorded signal becomes more spatially restricted. Separating in-focus information from out-of-focus light helps reveal cellular or tissue structures within the specimen.
Depth information is assembled through a z-stack, a series of optical sections collected at successive focal depths. Each section records structures at a particular position within the sample, while the complete sequence preserves their three-dimensional relationships. Computational reconstruction then turns the individual planes into a view of organization through the specimen.
Point-by-point laser scanning associates detected fluorescence with a defined location in the specimen. Repeating the scan at different focal depths extends that positional information through the sample, rather than limiting observation to one optical plane. This is especially relevant when biological structures overlap in a projected view but occupy different depths.
Fluorescence provides the signal that the microscope maps across optical sections. Consequently, the reconstructed image can show where a fluorescent protein or other fluorescent structure occurs within cells or tissues. The depth-resolved information also supports examination of cell architecture and tissue organization, connecting molecular localization with larger-scale biological structure.
A practical workflow begins with a fluorescent specimen, establishes a focal position, and scans the sample point by point with the focused laser. The microscope then records optical sections at successive depths. Those sections are assembled computationally into a three-dimensional representation that researchers can inspect for internal organization and spatial relationships.
The technique can provide information at several biological scales. In cells, it supports examination of architecture and protein localization; in tissues, it reveals organization across depth. These outputs help researchers relate the position of fluorescent structures to surrounding biological arrangements, making the approach useful when location within a complex specimen is scientifically important.
In biology, 3D confocal microscopy supports studies of development, disease mechanisms, cell interactions, and changes in complex biological samples. Its reconstructed views allow investigators to examine how structures are arranged within depth and how cellular or tissue organization relates to the biological process being studied.