Stereo Investigator Software
Stereo Investigator Software - Related Videos
10:22
Comprehensive Spatial Profiling of Species-agnostic Transcriptomes via Stereo-seq
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2025
This article presents a protocol to perform comprehensive spatial transcriptomic profiling of host, viral, fungal, and microbiome RNA from formalin-fixed paraffin-embedded tissue sections using Stereo-seq, which enables high-resolution mapping of diverse transcriptomes while preserving tissue architecture.
05:42
Elevated Plus Maze Test Combined with Video Tracking Software to Investigate the Anxiolytic Effect of Exogenous Ketogenic Supplements
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Cited by 39 •
2019
Here, we present a protocol to investigate changes in the anxiety level of rodent animal models. The elevated plus maze (EPM) test, used together with a video tracking software, provides a reliable method to document the effect of various potential anxiolytic treatments in preclinical laboratory scenarios.
14:14
Quantification of Strain in a Porcine Model of Skin Expansion Using Multi-View Stereo and Isogeometric Kinematics
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Cited by 9 •
2017
This protocol uses multi-view stereo to generate three-dimensional (3D) models out of uncalibrated sequences of photographs, making it affordable and adjustable to a surgical setting. Strain maps between the 3D models are quantified with spline-based isogeometric kinematics, which facilitate representation of smooth surfaces over coarse meshes sharing the same parameterization.
08:47
Automated Analysis of C. elegans Swim Behavior Using CeleST Software
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Cited by 18 •
2016
An efficient and simple methodology for computer-based analysis of nematode swimming behavior in liquid is described. The method requires little to no investment for C. elegans laboratories. The hardware used is standard, and the computer software for the behavioral analysis (CeleST) is an open source one.
10:41
VisualEyes: A Modular Software System for Oculomotor Experimentation
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Cited by 28 •
2011
Neural control and cognitive processes can be studied through eye movements. The VisualEyes software allows an operator to program stimuli on two computer screens independently using a simple, custom scripting language. The system can stimulate tandem eye movements (saccades and smooth pursuit) or opposing eye movements (vergence) or any combination.
FAQs
Systematic random sampling distributes observations across the tissue rather than relying on selectively chosen fields. This approach helps reduce sampling bias when estimating biological features from sections and supports more defensible comparisons between experimental groups. It is particularly important when cells, vessels, lesions, or other structures vary in location or density within an organ.
The optical disector and fractionator are stereological probes that connect sampled image regions with quantitative estimates. Their selection depends on the measurement goal, such as estimating cell numbers, volume, length, or spatial distribution. Using defined probes makes the analysis more structured and helps researchers apply consistent measurements across tissue samples and experimental conditions.
User-defined regions of interest restrict measurements to biologically relevant portions of an image or tissue section. This helps separate target structures from surrounding material and ensures that sampling and stereological measurements address the intended anatomical area. Consistent region selection also improves reproducibility when researchers compare different specimens, treatment groups, or tissue compartments.
A typical workflow links microscopy-based image acquisition with selection of relevant tissue regions, systematic random sampling, application of an appropriate stereological probe, and quantitative data analysis. Researchers then compare measurements across specimens or experimental groups. Keeping these stages connected supports reproducible assessment of cells, vessels, lesions, and other tissue features.
The platform supports quantitative studies of neurons, glial cells, blood vessels, lesions, and other tissue features. Its applications extend across neuroscience, pathology, developmental biology, and drug evaluation, where researchers need measurements from tissue sections rather than purely descriptive microscopy. The same analytical framework can support comparisons among organs, conditions, or experimental groups.
Researchers can obtain estimates of cell numbers, tissue or feature volumes, lengths, and spatial distributions. These outcomes allow biological groups to be compared using quantitative measurements rather than visual impressions alone. In brain and organ studies, such results can strengthen evaluations of anatomical change, pathology, development, or drug-related effects when sampling and analysis remain consistent.