Light is a complex phenomenon that is classically explained with a simple model based on rays and wavefronts. The Molecular Expressions Microscopy Primer explores many of the aspects of visible light starting with an introduction to electromagnetic radiation and continuing through to human vision and the perception of color. Each section outlined below is an independent treatise on a limited aspect of light and color. We hope you enjoy your visit and find the answers to your questions.

Electromagnetic Radiation - Visible light is a complex phenomenon that is classically explained with a simple model based on propagating rays and wavefronts, a concept first proposed in the late 1600s by Dutch physicist Christiaan Huygens. Electromagnetic radiation, the larger family of wave-like phenomena to which visible light belongs (also known as radiant energy), is the primary vehicle transporting energy through the vast reaches of the universe. The mechanisms by which visible light is emitted or absorbed by substances, and how it predictably reacts under varying conditions as it travels through space and the atmosphere, form the basis of the existence of color in our universe.

Light: Particle or a Wave? - Many distinguished scientists have attempted to explain how electromagnetic radiation can display what has now been termed duality, or both particle-like and wave-like behavior. At times light behaves as if composed of particles, and at other times as a continuous wave. This complementary, or dual, role for the properties of light can be employed to describe all of the known characteristics that have been observed experimentally, ranging from refraction, reflection, interference, and diffraction, to the results with polarized light and the photoelectric effect.

Sources of Visible Light - A wide variety of sources are responsible for emission of electromagnetic radiation, and are generally categorized according to the specific spectrum of wavelengths generated by the source. Relatively long radio waves are produced by electrical current flowing through huge broadcast antennas, while much shorter visible light waves are produced by the energy state fluctuations of negatively charged electrons within atoms. The shortest form of electromagnetic radiation, gamma waves, results from decay of nuclear components at the center of the atom. The visible light that humans are able to see is usually a mixture of wavelengths whose varying composition is a function of the light source.

Fluorescence - The phenomenon of fluorescence was known by the middle of the nineteenth century. British scientist Sir George G. Stokes first made the observation that the mineral fluorspar exhibits fluorescence when illuminated with ultraviolet light, and he coined the word "fluorescence". Stokes observed that the fluorescing light has longer wavelengths than the excitation light, a phenomenon that has become to be known as the Stokes shift. Fluorescence microscopy is an excellent method of studying material that can be made to fluoresce, either in its natural form (termed primary or auto fluorescence) or when treated with chemicals capable of fluorescing (known as secondary fluorescence). The fluorescence microscope was devised in the early part of the twentieth century by August Köhler, Carl Reichert, and Heinrich Lehmann, among others. However, the potential of this instrument was not realized for several decades, and fluorescence microscopy is now an important (and perhaps indispensable) tool in cellular biology.

Speed of Light - Starting with Ole Roemer's 1676 breakthrough endeavors, the speed of light has been measured at least 163 times by more than 100 investigators utilizing a wide variety of different techniques. Finally in 1983, more than 300 years after the first serious measurement attempt, the speed of light was defined as being 299,792.458 kilometers per second by the Seventeenth General Congress on Weights and Measures. Thus, the meter is defined as the distance light travels through a vacuum during a time interval of 1/299,792,458 seconds. In general, however, (even in many scientific calculations) the speed of light is rounded to 300,000 kilometers (or 186,000 miles) per second.

Reflection of Light - Reflection of light (and other forms of electromagnetic radiation) occurs when the waves encounter a surface or other boundary that does not absorb the energy of the radiation and bounces the waves away from the surface. The incoming light wave is referred to as an incident wave and the wave that is bounced away from the surface is called the reflected wave. The simplest example of visible light reflection is the glass-like surface of a smooth pool of water, where the light is reflected in an orderly manner to produce a clear image of the scenery surrounding the pool. Throw a rock into the pool, and the water is perturbed to form waves, which disrupt the image of the scene by scattering the reflected light in all directions.

Refraction of Light - As light passes from one substance into another, it will travel straight through with no change of direction when crossing the boundary between the two substances head-on (perpendicular, or a 90-degree angle of incidence). However, if the light impacts the boundary at any other angle it will be bent or refracted, with the degree of refraction increasing as the beam is progressively inclined at a greater angle with respect to the boundary. As an example, a beam of light striking water vertically will not be refracted, but if the beam enters the water at a slight angle it will be refracted to a very small degree. If the angle of the beam is increased even further, the light will refract with increasing proportion to the entry angle. Early scientists realized that the ratio between the angle at which the light crosses the media interface and the angle produced after refraction is a very precise characteristic of the material producing the refraction effect.

Diffraction of Light - Depending on the circumstances that give rise to the phenomenon, diffraction can be perceived in a variety of different ways. Scientists have cleverly utilized diffraction of neutrons and X-rays to elucidate the arrangement of atoms in small ionic crystals, molecules, and even such large macromolecular assemblies as proteins and nucleic acids. Electron diffraction is often employed to examine periodic features of viruses, membranes, and other biological organisms, as well as synthetic and naturally occurring materials. No lens exists that will focus neutrons and X-rays into an image, so investigators must reconstruct images of molecules and proteins from the diffraction patterns using sophisticated mathematical analysis. Fortunately, magnetic lenses can focus diffracted electrons in the electron microscope, and glass lenses are very useful for focusing diffracted light to form an optical image that can easily be viewed.

Polarization of Light - The human eye lacks the ability to distinguish between randomly oriented and polarized light, and plane-polarized light can only be detected through an intensity or color effect, for example, by reduced glare when wearing polarized sun glasses. In effect, humans cannot differentiate between the high contrast real images observed in a polarized light microscope and identical images of the same specimens captured digitally (or on film), and then projected onto a screen with light that is not polarized. The first clues to the existence of polarized light surfaced around 1669 when Erasmus Bartholin discovered that crystals of the mineral Iceland spar (more commonly referred to as calcite) produce a double image when objects are viewed through the crystals in transmitted light. During his experiments, Bartholin also observed a quite unusual phenomenon. When the calcite crystals are rotated about their axis, one of the images moves in a circle around the other, providing strong evidence that the crystals are somehow splitting the light into two different beams.

Fundamentals of Interference - The seemingly close relationship between diffraction and interference occurs because they are actually manifestations of the same physical process and produce ostensibly reciprocal effects. Most of us observe some type of optical interference almost every day, but usually do not realize the events in play behind the often-kaleidoscopic display of color produced when light waves interfere with each other. One of the best examples of interference is demonstrated by the light reflected from a film of oil floating on water. Another example is the thin film of a soap bubble, which reflects a spectrum of beautiful colors when illuminated by natural or artificial light sources.

Optical Birefringence - Anisotropic crystals, such as quartz, calcite, and tourmaline, have crystallographically distinct axes and interact with light by a mechanism that is dependent upon the orientation of the crystalline lattice with respect to the incident light angle. When light enters the optical axis of anisotropic crystals, it behaves in a manner similar to the interaction with isotropic crystals, and passes through at a single velocity. However, when light enters a non-equivalent axis, it is refracted into two rays each polarized with the vibration directions oriented at right angles to one another, and traveling at different velocities. This phenomenon is termed double refraction or birefringence and is exhibited to a greater or lesser degree in all anisotropic crystals.

Color Temperature - The concept of color temperature is of critical importance in photography and digital imaging, regardless of whether the image capture device is a camera, microscope, or telescope. A lack of proper color temperature balance between the microscope light source and the film emulsion or image sensor is the most common reason for unexpected color shifts in photomicrography and digital imaging. If the color temperature of the light source is too low for the film, photomicrographs will have an overall yellowish or reddish cast and will appear warm. On the other hand, when the color temperature of the light source is too high for the film, photomicrographs will have a blue cast and will appear cool. The degree of mismatch will determine the extent of these color shifts, with large discrepancies leading to extremes in color variations. Perhaps the best example is daylight film used in a microscope equipped with a tungsten-halogen illumination source without the benefit of color balancing filters. In this case, the photomicrographs will have a quite large color shift towards warmer reddish and yellowish hues. As problematic as these color shifts may seem, they are always easily corrected by the proper use of conversion and light balancing filters.

Primary Colors - The human eye is sensitive to a narrow band of electromagnetic radiation that lies in the wavelength range between 400 and 700 nanometers, commonly known as the visible light spectrum, which is the only source of color. When combined, all of the wavelengths present in visible light, about a third of the total spectral distribution that successfully passes through the Earth's atmosphere, form colorless white light that can be refracted and dispersed into its component colors by means of a prism. The colors red, green, and blue are classically considered the primary colors because they are fundamental to human vision. Light is perceived as white by humans when all three cone cell types are simultaneously stimulated by equal amounts of red, green, and blue light.

Light Filters - A majority of the common natural and artificial light sources emit a broad range of wavelengths that cover the entire visible light spectrum, with some extending into the ultraviolet and infrared regions as well. For simple lighting applications, such as interior room lights, flashlights, spot and automobile headlights, and a host of other consumer, business, and technical applications, the wide wavelength spectrum is acceptable and quite useful. However, in many cases it is desirable to narrow the wavelength range of light for specific applications that require a selected region of color or frequency. This task can be easily accomplished through the use of specialized filters that transmit some wavelengths and selectively absorb, reflect, refract, or diffract unwanted wavelengths.

Human Vision and Color Perception - Human stereo color vision is a very complex process that is not completely understood, despite hundreds of years of intense study and modeling. Vision involves the nearly simultaneous interaction of the two eyes and the brain through a network of neurons, receptors, and other specialized cells. The first steps in this sensory process are the stimulation of light receptors in the eyes, conversion of the light stimuli or images into signals, and transmission of electrical signals containing the vision information from each eye to the brain through the optic nerves. This information is processed in several stages, ultimately reaching the visual cortices of the cerebrum.

Light and Energy - Mankind has always been dependent upon energy from the sun's light both directly - for warmth, to dry clothing, to cook, and indirectly to provide food, water, and air. Our awareness of the value of the sun's rays revolves around the manner in which we benefit from the energy, but there are far more fundamental implications from the relationship between light and energy. Whether or not mankind devises ingenius mechanisms to harness the sun's energy, our planet and the changing environment contained within is naturally driven by the energy of sunlight.

Introduction to Lenses and Geometrical Optics - The action of a simple lens, similar to many of those used in the microscope, is governed by the principles of refraction and reflection and can be understood with the aid of a few simple rules about the geometry involved in tracing light rays through the lens. The basic concepts explored in this discussion, which are derived from the science of Geometrical Optics, will lead to an understanding of the magnification process, the properties of real and virtual images, and lens aberrations or defects.

Basic Properties of Mirrors - Reflection of light is an inherent and important fundamental property of mirrors, and is quantitatively gauged by the ratio between the amount of light reflected from the surface and that incident upon the surface, a term known as reflectivity. Mirrors of different design and construction vary widely in their reflectivity, from nearly 100 percent for highly-polished mirrors coated with metals that reflect visible and infrared wavelengths, to nearly zero for strongly absorbing materials.

Prisms and Beamsplitters - Prisms and beamsplitters are essential components that bend, split, reflect, and fold light through the pathways of both simple and sophisticated optical systems. Cut and ground to specific tolerances and exact angles, prisms are polished blocks of glass or other transparent materials that can be employed to deflect or deviate a light beam, rotate or invert an image, separate polarization states, or disperse light into its component wavelengths. Many prism designs can perform more than one function, which often includes changing the line of sight and simultaneously shortening the optical path, thus reducing the size of optical instruments.

Laser Fundamentals - Ordinary natural and artificial light is released by energy changes on the atomic and molecular level that occur without any outside intervention. A second type of light exists, however, and occurs when an atom or molecule retains its excess energy until stimulated to emit the energy in the form of light. Lasers are designed to produce and amplify this stimulated form of light into intense and focused beams. The word laser was coined as an acronym for Light Amplification by the Stimulated Emission of Radiation. The special nature of laser light has made laser technology a vital tool in nearly every aspect of everyday life including communications, entertainment, manufacturing, and medicine.

Light and Color Java Tutorials - Difficult concepts in the physics of light and the science of optics are much easier to understand with the aid of interactive tutorials that demonstrate various aspects of the principles involved. Check out these cool Java tutorial-applets that explore a wide range of concepts in light, color, and optics.

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