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Interactive Java Tutorials

Welcome to the Molecular Expressions Virtual Microscopy website. We invite you to visit the interactive Java-powered virtual microscopes that we have constructed. These virtual microscopes explore specimen focus, illumination intensity, magnification, and translation---operating essentially in a manner that is identical to real-life microscopes.

Scanning Electron Microscopy - (approximately a 20 second download on 28.8K modems) We have teamed up with award-winning electron microscopist Dennis Kunkel to produce a virtual Scanning Electron Microscope (vSEM). Visitors can adjust the focus, contrast, and magnification of microscopic creatures viewed at thousands of times their actual size.

Translational Microscopy - (approximately a 40 second download on 28.8K modems) This interactive Java tutorial simulates the scanning of a sample under the microscope at a fixed magnification. Students must first focus the sample (as is the case with a real microscope), then they are able move the sample in all directions to thoroughly explore the various features exhibited by the sample. Brightness (Intensity) and Zoom controls allow fine-tuning of the microscopic images.

Magnifying Microscopy - (approximately a 30 second download on 28.8K modems) This interactive Java tutorial explores the effect of increasing magnification (equivalent to changing microscope objectives) on the ability to resolve features in a sample. We provide actual size images of the sample so students can understand the dramatic increases in magnification of the samples they are examining. Each magnification is accompanied by a description of the features available at that resolution. Samples featured in this module include computer chips, Moon rocks, superconductors, and the surface of a Compact Disc.

Laser Scanning Confocal Microscopy - (approximately a 30 second download on 28.8K modems) Several methods have been developed to overcome the poor contrast inherent with imaging thick specimens in a conventional microscope. Specimens having a moderate degree of thickness (5 to 15 microns) will produce dramatically improved images with either confocal or deconvolution techniques. The thickest specimens (20 microns and above) will suffer from a tremendous amount of extraneous light in out-of-focus regions, and are probably best-imaged using confocal techniques. This tutorial explores imaging specimens through serial z-axis optical sections utilizing a virtual confocal microscope.

Microscopy of Silicon Artwork - (approximately a 40 second download on 28.8K modems) Study the appearance of silicon artwork under varying conditions of illumination with this interactive Java tutorial. Sliders control specimen focus, brightness, and magnification and radio buttons allow the visitor to toggle between brightfield, darkfield, and differential interference contrast illumination.

Phase Contrast Microscopy - (approximately a 45 second download on 28.8K modems) Explore how phase plate alignment with respect to the objective phase ring affects specimen contrast in phase contrast microscopy. This tutorial allows the visitor to adjust the positioning of the phase plate slits using a virtual phase telescope. Specimen illumination is adjustable via the microscope illumination voltage, and the magnification can be varied from 4x to 40x. A fine focus slider is also provided to optimize specimen focus. Samples featured in this tutorial include Chinese Hamster Ovary cells, Desmids, starfish embryos, cheek cells, neuroblastoma cells, and Orlon synthetic fibers.

Stereoscopic Zoom Microscopy - (approximately a 30 second download on 28.8K modems) Use the special zoom feature in this interactive tutorial to examine reflected light stereoscopic specimens at a variety of magnifications. Select new specimens from a pull-down menu and use sliders to set the microscope focus and lamp intensity to optimize appearance of the image. The magnification range for this microscope is 0.75x to 11.25x, which can be adjusted with a variable slider.

Reflected Light Confocal Microscopy - (approximately a 45-60 second download on 28.8K modems) Explore microscopy of integrated circuits using real-time confocal observations at a resolution of 0.18 microns with this interactive Java tutorial.

Integrated Circuit Inspection Microscopy - (approximately a 45 second download on 28.8K modems) Imagine yourself in a chip fab inspecting wafers with a reflected light microscope. This interactive Java tutorial explores the surface structure of integrated circuits using brightfield, darkfield, and/or differential interference contrast (DIC) microscopy. After choosing a chip to examine, the visitor can toggle between the different illumination modes, adjust the focus and brightness, and change the magnification.

Polarized Light Microscopy - When a birefringent material is placed between crossed polarizers in an optical microscope, light incident upon the material is split into two component beams whose amplitude and intensity vary depending upon the orientation angle between the polarizer and permitted vibration directions of the material. Use this link to explore our tutorials on polarized light microscopy.

Microscopy of the Silicon Zoo - This tutorial explores image changes during rotation of the polarizer in the light path of a differential interference contrast (DIC) reflected light microscope. While examining doodles on integrated circuits, we demonstrate how image contrast and color vary with rotation of the polarizer.

Hoffman Modulation Contrast Microscopy - Hoffman modulation contrast is an oblique illumination technique that allows microscopists to enhance contrast in semi-transparent phase objects, which are difficult to image using conventional brightfield microscopy. This interactive tutorial explores how rotation of the substage polarizing filter affects image contrast in Hoffman modulation contrast microscopy.

Rheinberg Illumination (Optical Staining) Microscopy - (approximately a 30 second download on 28.8Kb modems) This interactive tutorial demonstrates how changes in the color of central and annular filters affect sample and background color when using Rheinberg illumination as a contrast-enhancing method in optical microscopy. Visitors are able to adjust the color of both the central and annular filters to preview how samples will appear under illumination with the different filter combinations.

Differential Interference Contrast Microscopy (DIC) - (approximately a 15 to 45 second download on 28.8Kb modems) The DIC interactive Java tutorial explores how changes in the orientation the polarizer in a Senarmont compensation system will affect image contrast. Visitors are able to adjust a slider that simulates rotation of the polarizer and are able to see how this rotation enhances sample contrast.

Virtual Microscopy: Depth-of-Focus in Thick Samples - (approximately a 15 to 45 second download on 28.8Kb modems) This simulated-DIC interactive Java tutorial allows the visitor to investigate how microscope depth-of-focus can be modulated to bring various parts of a very thick specimen into sharp focus.

Fluorescence Microscopy with Multiple Fluorochromes - (approximately a 15 to 45 second download on 28.8Kb modems) Fluorescence microscopy takes advantage of emission spectral properties of fluorochrome dyes used to specifically stain various portions of a specimen. This tutorial explores how samples stained with multiple fluorochrome stains appear when excitation illumination is filtered through various fluorescence cubes.

Fluorescence Combination Microscopy - (approximately a 10 to 20 second download on 28.8Kb modems) This tutorial simulates the combination of fluorescence microscopy with either phase contrast or differential interference contrast (DIC) microscopy. The visitor can toggle between views of the various techniques separately or combined to produce increased contrast effects.

Contributing Authors

Mortimer Abramowitz - Olympus America, Inc., Two Corporate Center Drive., Melville, New York, 11747.

Matthew J. Parry-Hill and Michael W. Davidson - National High Magnetic Field Laboratory, 1800 East Paul Dirac Dr., The Florida State University, Tallahassee, Florida, 32310.


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