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Related Concept Videos

Imaging Biological Samples with Optical Microscopy01:18

Imaging Biological Samples with Optical Microscopy

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Optical microscopy uses optic principles to provide detailed images of samples. Antonie van Leeuwenhoek designed the first compound optical microscope in the 17th century to visualize blood cells, bacteria, and yeast cells. In 1830, Joseph Jackson Lister created an essentially modern light microscope. The 20th century saw the development of microscopes with enhanced magnification and resolution.
In optical microscopy, the specimen to be viewed is placed on a glass slide and clipped on the stage...
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Electron Microscope Tomography and Single-particle Reconstruction01:07

Electron Microscope Tomography and Single-particle Reconstruction

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Transmission electron microscopy (TEM) can be used to determine the 3D structure of biological samples with the help of techniques such as electron microscope tomography and single-particle reconstruction. While single-particle reconstruction can examine macromolecules and macromolecular complexes in vitro conditions only, tomography permits the study of cell components or small cells in vivo.
Electron Tomography
Electron tomography can be performed either in TEM or STEM (scanning transmission...
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Computed Tomography01:10

Computed Tomography

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Tomography refers to imaging by sections. Computed tomography (CT) is a non-invasive imaging technique that uses computers to analyze several cross-sectional X-rays to reveal minute details about structures in the body.
The technique was invented in the 1970s and is based on the principle that as X-rays pass through the body, they are absorbed or reflected at different levels. In the technique, a patient lies on a motorized platform while a computerized axial tomography (CAT) scanner rotates...
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Confocal Fluorescence Microscopy01:16

Confocal Fluorescence Microscopy

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Confocal microscopy is an advanced microscopic technique. The prime advantage of the confocal microscope over other microscopy techniques is its ability to block the out-of-focus light from the illuminated samples using pinholes. It is widely used with fluorescence optics to obtain high-resolution, sharp contrast images. Unlike optical microscopes, confocal microscopes use a focused beam of light laser to scan the entire sample surface at different z-planes. These microscopes are, therefore,...
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Phase Contrast and Differential Interference Contrast Microscopy01:26

Phase Contrast and Differential Interference Contrast Microscopy

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Phase-Contrast Microscopes
In-phase-contrast microscopes, interference between light directly passing through a cell and light refracted by cellular components is used to create high-contrast, high-resolution images without staining. It is the oldest and simplest type of microscope that creates an image by altering the wavelengths of light rays passing through the specimen. Altered wavelength paths are created using an annular stop in the condenser. The annular stop produces a hollow cone of...
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Total Internal Reflection Fluorescence Microscopy01:05

Total Internal Reflection Fluorescence Microscopy

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Total internal reflection fluorescence microscopy or TIRF is an advanced microscopic technique used to visualize fluorophores in samples close to a solid surface with a higher refractive index, such as a glass coverslip. TIRF only allows fluorophores in proximity to the solid surface to be excited. When light from a medium with a lower refractive index (such as air) hits the glass coverslip at a critical angle, the light undergoes total internal reflection stead of passing through the glass.
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Related Experiment Video

Updated: Jan 11, 2026

Multimodal Volumetric Retinal Imaging by Oblique Scanning Laser Ophthalmoscopy oSLO and Optical Coherence Tomography OCT
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Multimodal Volumetric Retinal Imaging by Oblique Scanning Laser Ophthalmoscopy oSLO and Optical Coherence Tomography OCT

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Vis-OCT Explorer: an open-source software for visible-light optical coherence tomography data processing.

Weijia Fan, Fengyuanshan Xu, Roman Kuranov

    Biorxiv : the Preprint Server for Biology
    |November 19, 2025
    PubMed
    Summary
    This summary is machine-generated.

    We developed Vis-OCT Explorer, an open-source software for visible-light optical coherence tomography (vis-OCT) image processing. This tool enhances image quality and ensures repeatable retinal thickness measurements, crucial for clinical applications.

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    Area of Science:

    • Ophthalmology
    • Biomedical Imaging
    • Optical Engineering

    Background:

    • Visible-light optical coherence tomography (vis-OCT) offers advanced retinal visualization.
    • High-quality vis-OCT image reconstruction necessitates specialized post-processing techniques like balanced detection.
    • A standardized, open-source software solution is critical for the clinical translation of vis-OCT technology.

    Purpose of the Study:

    • To develop and evaluate Vis-OCT Explorer, an open-source, Python-based software for processing vis-OCT images.
    • To implement advanced processing features including dual-spectrometer balanced detection and STFT-based dispersion compensation optimization.
    • To assess the software's performance in image reconstruction quality and the repeatability of retinal thickness measurements.

    Main Methods:

    • Developed Vis-OCT Explorer, a modular software with standard OCT processing (k-space resampling, dispersion compensation, FFT).
    • Integrated unique features: dual-spectrometer balanced detection and STFT for dispersion compensation optimization.
    • Evaluated reconstruction quality using a quality index and assessed measurement repeatability with intraclass correlation coefficient (ICC) analysis across multiple operators and sites.

    Main Results:

    • Balanced detection and STFT-based dispersion compensation significantly improved the quality index of reconstructed B-scan images.
    • High repeatability (ICC > 0.8) for retinal nerve fiber layer (RNFL) and ganglion cell-inner plexiform layer (GCIPL) thickness measurements was achieved in 87.5% of macular-centered images.
    • Excellent repeatability (ICC > 0.8) for RNFL thickness measurements was observed across all optic nerve head-centered images.

    Conclusions:

    • Vis-OCT Explorer delivers high-quality image processing for vis-OCT human retinal images.
    • The software enables highly repeatable retinal thickness measurements, supporting clinical validation.
    • This tool is essential for facilitating multicenter clinical trials to establish vis-OCT's efficacy.