Volume Scan Protocol
Volume Scan Protocol - Related Videos
07:19
Clock Scan Protocol for Image Analysis: ImageJ Plugins
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Cited by 16 •
2017
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.
10:25
Specimen Preparation, Imaging, and Analysis Protocols for Knife-edge Scanning Microscopy
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Cited by 15 •
2011
The full process from brain specimen preparation to serial sectioning imaging using the Knife-Edge Scanning Microscope, to data visualization and analysis is described. This technique is currently used to acquire mouse brain data, but it is applicable to other organs, other species.
09:47
Array Tomography Workflow for the Targeted Acquisition of Volume Information using Scanning Electron Microscopy
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Cited by 16 •
2021
We describe the preparation of ribbons of serial sections and their collection on large transfer support for use as Array Tomography samples, along with automated imaging procedures in a scanning electron microscope. The protocol allows screening, retrieval, and targeted imaging of local, rare events, and the acquisition of large data volumes.
10:57
Scanning Electron Microscopy (SEM) Protocols for Problematic Plant, Oomycete, and Fungal Samples
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Cited by 19 •
2017
Problems in the processing of biological samples for scanning electron microscopy observation include cell collapse, treatment of samples from wet microenvironments and cell destruction. Low-cost and relatively rapid protocols suited for preparing challenging samples such as floral meristems, oomycete cysts, and fungi (Agaricales) are compiled and detailed here.
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...
FAQs
The sampling interval determines how densely the defined region is represented in depth. Smaller intervals provide more closely spaced optical sections, whereas larger intervals reduce the number of measurements and may provide less detailed representation of changes between sections. Keeping that interval consistent across specimens helps ensure that apparent differences in pathogen or immune-cell distribution reflect biology rather than unequal sampling.
Standardized acquisition settings are important because they make volumetric datasets comparable. If scan conditions or sampling intervals vary between specimens, differences in signal distribution or tissue appearance can be difficult to separate from technical variation. Applying the same protocol across treatment groups and time points supports more reliable comparisons of pathogen localization, tissue changes, and immune-cell infiltration.
Sequential optical sections preserve depth-resolved information that a single image plane cannot provide. Once assembled, the dataset can show whether a signal is localized, dispersed, or associated with particular regions throughout the sampled volume. This perspective is especially useful when infection-related changes or immune-cell infiltration vary with depth rather than appearing uniformly in one plane.
A practical workflow begins by defining the three-dimensional region to be examined and selecting the depth-sampling interval. The system then acquires sequential optical sections or other depth-resolved measurements throughout that region. Those sections are assembled into a volumetric dataset, which can be visualized and analyzed using the same acquisition and sampling parameters applied to other specimens.
In infection research, the resulting volume can be examined for pathogen distribution and tissue changes across the sampled region. In immunology, it can help assess where immune cells are located and whether infiltration varies within the tissue. These measurements support comparisons among specimens, treatment groups, and time points, linking spatial organization with experimental condition.
A single plane can show structures or signals at one depth, but it cannot reveal how those features are distributed through the full sampled region. Volume scanning extends the observation across depth, allowing researchers to evaluate spatial patterns such as localized pathogen presence, tissue alterations, or immune-cell infiltration. It therefore provides context that a one-plane measurement may miss.