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Confocal Microscopy Interactive Tutorials

Section Overview:

Explanations for many of the exceedingly complex concepts in laser scanning confocal microscopy can significantly benefit from the assistance of interactive tutorials that enable the student to obtain instantaneous (real-time) response to changes in variables. The tutorials in section address the basic aspects of confocal microscopy instrumentation, laser systems, detectors, image processing, resolution, contrast, and many other aspects of the technique. All interactive Java tutorials require the Java Virtual Machine, which is available without cost as a browser plug-in from Sun Microsystems.

Confocal Microscope Simulators

Confocal Microscope Systems

  • Laser Confocal Microscopy Scanning Modes

    Laser scanning modes enable investigators to optimize data collection for three-dimensional imaging. Examine various scanning mechanisms in confocal microscopy utilizing a cube-shaped virtual specimen.

  • Galvanometer-Based Confocal Scanning Systems

    Explore how the scanning mirrors are coordinated to direct the laser beam into the objective, and then to reflect secondary fluorescence to the emission filter.

  • Scanning System Basics

    Examine how the galvanometer-driven mirrors and optical system of a confocal microscope are configured to enable the objective rear aperture to be continuously filled with light during the raster scanning operation in this tutorial.

  • Laser Scanning Confocal Microscopy

    Explore imaging specimens through serial z-axis optical sections utilizing a virtual confocal microscope in this interactive tutorial.

Lasers for Confocal Microscopy

  • Diode Lasers

    Learn more in this interactive tutorial about semiconductor diode lasers having sufficient power output can be useful in optical microscopy.

  • Acousto-Optic Tunable Filters

    Explore more about electro-optic devices, such as the acousto-optic tunable filter (AOTF), which are commonly employed to modulate the wavelength and amplitude of illuminating laser light in confocal microscopes.

  • Stimulated Emission in a Laser Cavity

    Discover how laser amplification occurs starting from spontaneous emission of the first photon to saturation of the laser cavity and the establishment of a dynamic equilibrium state in this interactive tutorial.

  • Pockels Cell Laser Modulators

    The beam intensity of lasers can be stabilized by electronic control of the tube current or utilization of external components. Examine how the Pockels cell modulator operates to stabilize laser beam intensity.

  • Laser Energy Levels

    Population inversion can be produced in a laser through two basic mechanisms. Explore metastable states for both three-level and four-level laser systems in this interactive java tutorial.

  • Laser Cavity Resonance Modes and Gain Bandwidth

    Explore how varying the appropriate frequencies can alter curves describing the number of cavity modes and gain bandwidth of a laser in this featured interactive java tutorial.

  • Helium-Neon Lasers

    Learn more about this previously widely utilized laser system with compact size dimensions, helium-neon laser, in this interactive tutorial.
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  • Krypton-Argon Lasers

    Discover and learn more in this interactive tutorial as it simulates the three major spectral lines produced by a krypton-argon mixed-gas laser used in confocal microscopy.
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  • Argon-Ion Lasers

    Learn more in this tutorial about the well-explored family of ion lasers and how the argon-ion laser operates in the visible and ultraviolet spectral regions by utilizing an ionized species of the noble gas argon.

  • Helium-Cadmium Lasers

    Explore a simplified model of the helium-cadmium laser cavity operation by using a cutaway drawing of a helium-cadmium laser illustrated in the central window in this interactive tutorial.

Fluorophores for Confocal Microscopy

Resolution, Contrast, and Sampling in Confocal Microscopy

  • Airy Pattern Basics

    This tutorial explores how Airy pattern size changes with objective numerical aperture and the wavelength of illumination; it also simulates the close approach of two Airy patterns.

  • Airy Patterns and the Rayleigh Criterion

    This tutorial examines how Airy disk sizes, at the limit of optical resolution, vary with changes in objective numerical aperture and illumination wavelength and how these changes affect the resolution of the objective.

  • Airy Patterns and Resolution Criteria (3-D Version)

    Explore with a three-dimensional model how Airy disk sizes, at the limit of optical resolution, vary with changes in objective numerical aperture and illumination wavelength.

  • Reflected Confocal Microscopy: Integrated Circuit Inspection

    Examine layers on the surface of integrated circuits with this tutorial as it simulates imaging of integrated circuits using a reflected light Nipkow disk Confocal Microscope.

Confocal Microscope Detectors

  • Side-On Photomultipliers

    In the side-on photomultiplier tube design, photons impact an internal photocathode and eject electrons from the front face (as opposed to the rear side as in the end-on designs) as shown in this tutorial.

  • Channel Photomultipliers

    Each time an electron impacts an inner wall of the channel, multiple secondary electrons are emitted. Learn and explore how electrons are multiplied within the conductive chain of a channel photomultiplier in this interactive tutorial.

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