Z-stack Scanning
Z-stack Scanning - Related Videos
09:38
Scaling of Engineered Vascular Grafts Using 3D Printed Guides and the Ring Stacking Method
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Cited by 6 •
2017
Scalable engineered blood vessels would improve clinical applicability. Using easily sizable 3D-printed guides, rings of vascular smooth muscle were created and stacked into a tubular form, forming a vascular graft. Grafts can be sized to meet the range of human coronary artery dimensions by simply changing the 3D-printed guide size.
02:28
Leaky Scanning
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2020
During most eukaryotic translation processes, the small 40S ribosome subunit scans an mRNA from its 5' end until it encounters the first start AUG codon. The large 60S ribosomal subunit then joins the smaller one to initiate protein synthesis. The location of the translation initiation is largely determined by the nucleotides near the start codon as there may be multiple translation initiation sites present on the mRNA. Marilyn Kozak discovered that the sequence RCCAUGG (where R stands for...
07:19
Clock Scan Protocol for Image Analysis: ImageJ Plugins
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Cited by 16 •
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This paper describes two novel ImageJ plugins for 'Clock Scan' image analysis. These plugins expand the functionality of the original visual basic 6 program and, most importantly, make the program available to a large research community by bundling it with the ImageJ free image analysis software package.
12:03
Differential Scanning Calorimetry
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2023
Source: Danielle N. Beatty and Taylor D. Sparks, Department of Materials Science and Engineering, The University of Utah, Salt Lake City, UT Differential scanning calorimetry (DSC) is an important measurement to characterize thermal properties of materials. DSC is used primarily to calculate the amount of heat stored in a material as it heats up (heat capacity) as well as the heat absorbed or released during chemical reactions or phase changes. However, measurement of this heat can also lead to...
07:47
Analysis of Brain Mitochondria Using Serial Block-Face Scanning Electron Microscopy
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Cited by 32 •
2016
Mitochondrial visualization and analysis from mammalian brain tissue is a challenging task. Here, we describe how three dimensional (3D) reconstruction analysis from the serial block-face scanning electron microscopy (SBFSEM) can be used to gain insights on the morphological and volumetric analysis of this critical energy generating organelle.
FAQs
The focal-plane interval determines how frequently images are collected through the selected depth. Regularly spaced sections give the reconstruction software the sequential information needed to represent structures across that range. A defined interval is therefore important when examining the relative position of immune cells, pathogens, or tissue features, because uneven or insufficient sampling can make spatial relationships harder to interpret.
Optical sections separate information from different focal planes, allowing features located at different depths to be examined individually before they are combined computationally. This helps distinguish overlapping cells, pathogens, or tissue structures that may appear superimposed in one image. In infection studies, that added depth information can clarify whether signals occupy the same region or occur at different positions.
Both representations are generated from the acquired optical sections, but they organize the depth information differently. A three-dimensional reconstruction is used to examine structure through the sampled volume, whereas a projection combines the sections into a composite view. Selecting between them depends on whether the analysis emphasizes spatial organization across depth or a consolidated visualization of the specimen.
The useful depth range is set by the portion of the specimen selected for acquisition and by the sequence of focal planes recorded across that region. Scanning too narrow a depth may omit relevant structures, while scanning beyond the region of interest can add images without improving the specific analysis. Defining the depth deliberately supports clearer interpretation of tissue architecture and localization.
First, select the specimen region and define the depth to be examined. The microscope then moves the focal plane through that depth at regular intervals while recording two-dimensional images. Software combines the resulting optical sections into a three-dimensional reconstruction or projection. Researchers can then inspect localization, morphology, spatial distribution, and relationships among structures within the sampled volume.
It is especially useful when immune cells, pathogens, and tissue architecture occupy different positions within a complex sample. A single focal plane may obscure these relationships, whereas depth-resolved imaging can reveal where infection is distributed and how cells are arranged around it. The resulting spatial information supports examination of host-pathogen relationships and cell-cell interactions.
Image stacks can support analysis of where labeled or recognizable structures are located, how their morphology changes through depth, and how they relate spatially to neighboring features. In immunology and infection studies, this includes examining pathogen distribution, immune-cell positioning, tissue organization, and apparent cell-cell interactions. These observations connect microscopic structure with the organization of the infected sample.
Host-pathogen relationships often depend on spatial context rather than signal observed in isolation. By examining successive focal planes and their combined representation, researchers can determine how pathogens are positioned relative to immune cells and surrounding tissue architecture. This can reveal patterns of localization and interaction that a single image might conceal, strengthening interpretation of infection within complex specimens.