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Laser Scanning Confocal Microscopy

Confocal microscopy offers several advantages over conventional optical microscopy, including controllable depth of field, the elimination of image degrading out-of-focus information, and the ability to collect serial optical sections from thick specimens. The key to the confocal approach is the use of spatial filtering to eliminate out-of-focus light or flare in specimens that are thicker than the plane of focus. There has been a tremendous explosion in the popularity of confocal microscopy in recent years, due in part to the relative ease with which extremely high-quality images can be obtained from specimens prepared for conventional optical microscopy, and in its great number of applications in many areas of current research interest. Visit the Molecular Expressions and Nikon MicroscopyU articles, galleries, interactive tutorials, and Web references using the links provided below.

Laser Scanning Confocal Microscope Simulator - Perhaps the most significant advance in optical microscopy during the past decade has been the refinement of mainstream laser scanning confocal microscope (LSCM) techniques using improved synthetic fluorescent probes and genetically engineered proteins, a wider spectrum of laser light sources coupled to highly accurate acousto-optic tunable filter control, and the combination of more advanced software packages with modern high-performance computers. This interactive tutorial explores multi-laser fluorescence and differential interference contrast (DIC) confocal imaging using the Olympus FluoView FV1000 confocal microscope software interface as a model.

Introduction to Confocal Microscopy - Confocal microscopy offers several advantages over conventional widefield optical microscopy, including the ability to control depth of field, elimination or reduction of background information away from the focal plane (that leads to image degradation), and the capability to collect serial optical sections from thick specimens. The basic key to the confocal approach is the use of spatial filtering techniques to eliminate out-of-focus light or glare in specimens whose thickness exceeds the immediate plane of focus. There has been a tremendous explosion in the popularity of confocal microscopy in recent years, due in part to the relative ease with which extremely high-quality images can be obtained from specimens prepared for conventional fluorescence microscopy, and the growing number of applications in cell biology that rely on imaging both fixed and living cells and tissues. In fact, confocal technology is proving to be one of the most important advances ever achieved in optical microscopy.

Basic Concepts - Current instruments are highly evolved from the earliest versions, but the principle of confocal imaging advanced by Marvin Minsky, and patented in 1957, is employed in all modern confocal microscopes. In a conventional widefield microscope, the entire specimen is bathed in light from a mercury or xenon source, and the image can be viewed directly by eye or projected onto an image capture device or photographic film. In contrast, the method of image formation in a confocal microscope is fundamentally different. Illumination is achieved by scanning one or more focused beams of light, usually from a laser or arc-discharge source, across the specimen. This point of illumination is brought to focus in the specimen by the objective lens, and laterally scanned using some form of scanning device under computer control. The sequences of points of light from the specimen are detected by a photomultiplier tube (PMT) through a pinhole (or in some cases, a slit), and the output from the PMT is built into an image and displayed by the computer. Although unstained specimens can be viewed using light reflected back from the specimen, they usually are labeled with one or more fluorescent probes.

Imaging Modes - A number of different imaging modes are used in the application of confocal microscopy to a vast variety of specimen types. They all rely on the ability of the technique to produce high-resolution images, termed optical sections, in sequence through relatively thick sections or whole-mount specimens. Based on the optical section as the basic image unit, data can be collected from fixed and stained specimens in single, double, triple, or multiple-wavelength illumination modes, and the images collected with the various illumination and labeling strategies will be in register with each other. Live cell imaging and time-lapse sequences are possible, and digital image processing methods applied to sequences of images allow z-series and three-dimensional representation of specimens, as well as the time-sequence presentation of 3D data as four-dimensional imaging. Reflected light imaging was the mode used in early confocal instruments, but any of the transmitted light imaging modes commonly employed in microscopy can be utilized in the laser scanning confocal microscope.

Specimen Preparation and Imaging - The procedures for preparing and imaging specimens in the confocal microscope are largely derived from those that have been developed over many years for use with the conventional wide field microscope. In the biomedical sciences, a major application of confocal microscopy involves imaging either fixed or living cells and tissues that have usually been labeled with one or more fluorescent probes. A large number of fluorescent probes are available that, when incorporated in relatively simple protocols, specifically stain certain cellular organelles and structures. Among the plethora of available probes are dyes that label nuclei, the Golgi apparatus, the endoplasmic reticulum, and mitochondria, and also dyes such as fluorescently labeled phalloidins that target polymerized actin in cells. Regardless of the specimen preparation protocol employed, a primary benefit of the manner in which confocal microscopy is carried out is the flexibility in image display and analysis that results from the simultaneous collection of multiple images, in digital form, into a computer.

Fluorophores for Confocal Microscopy - Biological laser scanning confocal microscopy relies heavily on fluorescence as an imaging mode, primarily due to the high degree of sensitivity afforded by the technique coupled with the ability to specifically target structural components and dynamic processes in chemically fixed as well as living cells and tissues. Many fluorescent probes are constructed around synthetic aromatic organic chemicals designed to bind with a biological macromolecule (for example, a protein or nucleic acid) or to localize within a specific structural region, such as the cytoskeleton, mitochondria, Golgi apparatus, endoplasmic reticulum, and nucleus. Other probes are employed to monitor dynamic processes and localized environmental variables, including concentrations of inorganic metallic ions, pH, reactive oxygen species, and membrane potential. Fluorescent dyes are also useful in monitoring cellular integrity (live versus dead and apoptosis), endocytosis, exocytosis, membrane fluidity, protein trafficking, signal transduction, and enzymatic activity. In addition, fluorescent probes have been widely applied to genetic mapping and chromosome analysis in the field of molecular genetics.

Spectral Bleed-Through Artifacts in Confocal Microscopy - The spectral bleed-through of fluorescence emission (often termed crossover or crosstalk), which occurs due to the very broad bandwidths and asymmetrical spectral profiles exhibited by many of the common fluorophores, is a fundamental problem that must be addressed in both widefield and laser scanning confocal fluorescence microscopy. The phenomenon is usually manifested by the emission of one fluorophore being detected in the photomultiplier channel or through the filter combination reserved for a second fluorophore. Bleed-through artifacts often complicate the interpretation of experimental results, particularly if subcellular colocalization of fluorophores is under investigation or quantitative measurements are necessary, such as in resonance energy transfer (FRET) and photobleaching (FRAP) studies.

Choosing Fluorophore Combinations for Confocal Microscopy - In planning multiple label fluorescence staining protocols for widefield and laser scanning confocal fluorescence microscopy experiments, the judicious choice of probes is paramount in obtaining the best target signal while simultaneously minimizing bleed-through artifacts. This interactive tutorial is designed to explore the matching of dual fluorophores with efficient laser excitation lines, calculation of emission spectral overlap values, and determination of the approximate bleed-through level that can be expected as a function of the detection window wavelength profiles.

Laser Systems for Optical Microscopy - The lasers commonly employed in optical microscopy are high-intensity monochromatic light sources, which are useful as tools for a variety of techniques including optical trapping, lifetime imaging studies, photobleaching recovery, and total internal reflection fluorescence. In addition, lasers are also the most common light source for scanning confocal fluorescence microscopy, and have been utilized, although less frequently, in conventional widefield fluorescence investigations.

Laser Safety - The two major concerns in safe laser operation are exposure to the beam and the electrical hazards associated with high voltages within the laser and its power supply. While there are no known cases of a laser beam contributing to a person's death, there have been several instances of deaths attributable to contact with high voltage laser-related components. Beams of sufficiently high power can burn the skin, or in some cases create a hazard by burning or damaging other materials, but the primary concern with regard to the laser beam is potential damage to the eyes, which are the part of the body most sensitive to light.

Acousto-Optic Tunable Filters (AOTFs) - Several benefits of the AOTF combine to greatly enhance the versatility of the latest generation of confocal instruments, and these devices are becoming increasing popular for control of excitation wavelength ranges and intensity. The primary characteristic that facilitates nearly every advantage of the AOTF is its capability to allow the microscopist control of the intensity and/or illumination wavelength on a pixel-by-pixel basis while maintaining a high scan rate. This single feature translates into a wide variety of useful analytical microscopy tools, which are even further enhanced in flexibility when laser illumination is employed.

Resolution and Contrast in Confocal Microscopy - All optical microscopes, including conventional widefield, confocal, and two-photon instruments are limited by fundamental physical factors in the resolution that they can achieve. In a perfect optical system, resolution is limited by numerical aperture of the optical components and by the wavelength of the light, both incident and detected. The concept of resolution is inseparable from contrast, and is defined as the minimum separation between two points that results in a certain contrast between them. In a real fluorescence microscope, contrast is determined by the number of photons collected from the specimen, the dynamic range of the signal, optical aberrations of the imaging system, and the number of picture elements (pixels) per unit area.

Non-Coherent Light Sources for Confocal Microscopy - The traditional illumination system in the modern widefield microscope utilizes a tungsten-halogen source for transmitted light and a short-arc lamp for fluorescence excitation. Various lasers have been utilized as a light source for widefield observation by a few investigators, but the advent of the confocal microscope vastly increased laser use in microscopy. This discussion reviews the merits and limitations of non-coherent (or non-laser) light sources in confocal microscopy, both as light sources for confocal illumination and as secondary sources for widefield microscopy in confocal microscopes. Two initial issues frequently arise when illumination systems for confocal microscopes are considered, and these have a direct bearing on the choice of light sources for a particular instrument.

Confocal Microscope Objectives - For any conventional optical microscope configuration, the objective is the most critical component of the system in determining the information content of the image. The contrast and resolution of fine specimen detail, the depth within the specimen from which information can be obtained, and the lateral extent of the image field are all determined by the design of the objective and its performance under the specific conditions employed for the observation. Additional demands are imposed on the objective in scanning confocal techniques, in which this crucial imaging component also serves as the illumination condenser and is often required to perform with high precision at a wide range of wavelengths and at very low light levels without introducing unacceptable image-degrading noise.

Confocal Microscope Scanning Systems - Confocal imaging relies upon the sequential collection of light from spatially filtered individual specimen points, followed by electronic signal processing and ultimately, the visual display as corresponding image points. The point-by-point signal collection process requires a mechanism for scanning the focused illuminating beam through the specimen volume under observation. Three principal scanning variations are commonly employed to produce confocal microscope images. Fundamentally equivalent confocal operation can be achieved by employing a laterally translating specimen stage coupled to a stationary illuminating light beam (stage scanning), a scanned light beam with a stationary stage (beam scanning), or by maintaining both the stage and light source stationary while scanning the specimen with an array of light points transmitted through apertures in a spinning Nipkow disk. Each technique has performance features that make it advantageous for specific confocal applications, but that limit the usefulness in others.

Signal-to-Noise Considerations - In any quantitative assessment of imaging capabilities utilizing digital microscopy techniques, including confocal methods, the effect of signal sampling on contrast and resolution must be considered. The measured signal level values do not directly represent the number of photons emitted or scattered by the specimen, but are proportional to that number. Furthermore, each individual sample of signal intensity is only an approximation of the number of collected photons, and will vary with repeated measurement. The variation, referred to as noise, imparts an uncertainty in the quantification of intensity, and therefore in the contrast and resolution of the image data.

Electronic Light Detectors: Photomultipliers - In modern widefield fluorescence and laser scanning confocal optical microscopy, the collection and measurement of secondary emission gathered by the objective can be accomplished by several classes of photosensitive detectors, including photomultipliers, photodiodes, and solid-state charge-coupled devices (CCDs). In confocal microscopy, fluorescence emission is directed through a pinhole aperture positioned near the image plane to exclude light from fluorescent structures located away from the objective focal plane, thus reducing the amount of light available for image formation. As a result, the exceedingly low light levels most often encountered in confocal microscopy necessitate the use of highly sensitive photon detectors that do not require spatial discrimination, but instead respond very quickly with a high level of sensitivity to a continuous flux of varying light intensity.

Critical Aspects of Confocal Microscopy - Quantitative three-dimensional imaging in fluorescence microscopy is often complicated by artifacts due to specimen preparation, controllable and uncontrollable experimental variables, or configuration problems with the microscope. This article, written by Dr. James B. Pawley, catalogs the most common extraneous factors that often serve to obscure results collected in fluorescence widefield and confocal microscopy. Among the topics discussed are the laser system, optical component alignment, objective magnification, bleaching artifacts, aberrations, immersion oil, coverslip thickness, quantum efficiency, and the specimen embedding medium.

Aberrations in Multicolor Confocal Microscopy - Refinements in design have simplified confocal microscopy to the extent that it has become a standard research tool in cell biology. However, as confocal microscopes have become more powerful, they have also become more demanding of their optical components. In fact, optical aberrations that cause subtle defects in image quality in widefield microscopy can have devastating effects in confocal microscopy. Unfortunately, the exacting optical requirements of confocal microscopy are often hidden by the optical system that guarantees a sharp image, even when the microscope is performing poorly. Optics manufacturers provide a wide range of microscope objectives, each designed for specific applications. This report demonstrates how the trade-offs involved in objective design can affect confocal microscopy.

Three-Color Imaging for Confocal Microscopy - The laser scanning confocal microscope (LSCM) is routinely used to produce digital images of single-, double-, and triple-labeled fluorescent samples. The use of red, green and blue (RGB) color is most informative for displaying the distribution of up to three fluorescent probes labeling a cell, where any colocalization is observed as a different additive color when the images are colorized and merged into a single three-color image. In this section we present a simplified version of a previously published method for producing three-color confocal images using the popular image manipulation program, Adobe Photoshop. In addition, several applications of the three-color merging protocol for displaying confocal images are discussed. Note that these digital methods are not confined to images produced using the LSCM and can be applied to digital images imported into Photoshop from many different sources.

Basics of Confocal Reflection Microscopy - Confocal reflection microscopy can be utilized to gather additional information from a specimen with relatively little extra effort, since the technique requires minimum specimen preparation and instrument re-configuration. In addition, information from unstained tissues is readily available with confocal reflection microscopy, as is data from tissues labeled with probes that reflect light. The method can also be utilized in combination with more common classical fluorescence techniques. Examples of the latter application are detection of unlabeled cells in a population of fluorescently labeled cells and for imaging the interactions between fluorescently labeled cells growing on opaque, patterned substrata.

Applications in Confocal Microscopy - The broad range of applications available to laser scanning confocal microscopy includes a wide variety of studies in neuroanatomy and neurophysiology, as well as morphological studies of a wide spectrum of cells and tissues. In addition, the growing use of new fluorescent proteins is rapidly expanding the number of original research reports coupling these useful tools to modern microscopic investigations. Other applications include resonance energy transfer, stem cell research, photobleaching studies, lifetime imaging, multiphoton microscopy, total internal reflection, DNA hybridization, membrane and ion probes, bioluminescent proteins, and epitope tagging. Many of these powerful techniques are described in these reviews.

Confocal Microscopy Image Gallery - The Nikon MicroscopyU Confocal Image Gallery features digital image sequences captured using a Nikon PCM-2000 confocal microscope scanning system coupled to an Eclipse E-600 upright microscope. Successive serial optical sections were recorded along the optical axis of the microscope over a range of specimen planes. These sequences are presented as interactive Java tutorials that allow the visitor to either "play" the series of sections automatically, or to utilize a slider to scroll back and forth through the images.

Olympus FluoView Laser Scanning Confocal Microscopy - The new Olympus FluoViewTM FV1000 is the latest in point-scanning, point-detection, confocal laser scanning microscopes designed for today's intensive and demanding biological research investigations. Excellent resolution, bright and crisp optics, and high efficiency of excitation, coupled to an intuitive user interface and affordability are key characteristics of this state-of-the-art optical microscopy system.

Marvin Lee Minsky (1927-Present) - While at Harvard University, Marvin Minsky made his primary contribution to the field of optics by inventing the confocal scanning microscope. Despite the theoretical benefits of the confocal approach for biological purposes, Minsky's microscope originally generated little interest. In hindsight it has become apparent that the technology of the period limited Minsky's demonstration of the potential of the confocal approach. Yet, years later, with the advent of such applicable devices as lasers, sensitive low-noise photodetectors, and fast microcomputers with image processing capabilities, Minsky's microscopy technique has become widespread in biological research.

Interactive Java Tutorials

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 with 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.

Comparing Confocal and Widefield Fluorescence Microscopy - Confocal microscopy offers several distinct advantages over traditional widefield fluorescence microscopy, including the ability to control depth of field, elimination or reduction of background information away from the focal plane (that leads to image degradation), and the capability to collect serial optical sections from thick specimens. The basic key to the confocal approach is the use of spatial filtering techniques to eliminate out-of-focus light or glare in specimens whose thickness exceeds the dimensions of the focal plane. This interactive tutorial explores and compares the differences between specimens when viewed in a confocal versus a widefield fluorescence microscope.

Colocalization of Fluorophores in Confocal Microscopy - Two or more fluorescence emission signals can often overlap in digital images recorded by confocal microscopy due to their close proximity within the specimen. This effect is known as colocalization and usually occurs when fluorescently labeled molecules bind to targets that lie in very close or identical spatial positions. This interactive tutorial explores the quantitative analysis of colocalization in a wide spectrum of specimens that were specifically designed either to demonstrate the phenomenon, or to alternatively provide examples of fluorophore targets that lack any significant degree of colocalization.

Reflected Confocal Microscopy: Integrated Circuit Inspection - Examine individual layers on the surface of integrated circuits with this interactive tutorial. Digital images for the tutorial were collected with a Nikon Optiphot C200 reflected light confocal microscope. For each sequence, a series of z-axis optical sections was recorded as the microscope was successively focused (at 1-micrometer steps) deeper within the patchwork of circuitry on the surface of the silicon chips.

Excitation Photobleaching Patterns - Multiphoton fluorescence microscopy utilizes diffraction-limited focusing by a high numerical aperture objective to localize the spatial concentration of excitation light to narrow region near the focal point. In contrast, the excitation region of a laser scanning confocal microscope is similar to that of a widefield microscope. This tutorial compares excitation-induced photobleaching patterns that occur near the focal region in both multiphoton and confocal microscopy systems.

Olympus FluoView Resource Center Interactive Java Tutorials - 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 instanteous (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.

References and Resources

Recommended Books on Confocal Microscopy - A surprisingly limited number of books dealing with various aspects of laser scanning and spinning disk confocal microscopy and related techniques are currently available from the booksellers. This section lists the FluoView Resource Center website development team's top 12 recommended books. Although the volumes listed in this section deal pricipally with confocal microscopy and related methodology, there exist a number of additional books that contain focused treatments of the materials described below, and these should also be consulted for specific techniques and timely review articles.

ZEISS Campus Confocal Microscopy Reference Library - A majority of the literature pertaining to review articles on laser scanning confocal microscopy has been published in textbooks, edited article collections, and symposia, with only an intermittent sprinkling of papers in the scientific journals. The reviews listed in this section should be available to students and investigators who have access to subscriptions through their host institutions.

Confocal Microscopy Web Resources - Laser scanning confocal microscopy (LSCM), a tool that has been extensively utilized for inspection of semiconductors, is now becoming a mainstream application in cell biology. The links provided in this section from the Molecular Expressions web site offer tutorials, instrumentation, application notes, technical support, glossaries, and reference materials on confocal microscopy and related techniques.

Basic Concepts in Laser Scanning Confocal Microscopy (PDF; 2.8 Mb) - Laser scanning confocal microscopy has become an invaluable tool for a wide range of investigations in the biological and medical sciences for imaging thin optical sections in living and fixed specimens ranging in thickness up to 100 micrometers. Modern instruments are equipped with 3-5 laser systems controlled by high-speed acousto-optic tunable filters (AOTFs), which allow very precise regulation of wavelength and excitation intensity. Coupled with photomultipliers that have high quantum efficiency in the near-ultraviolet, visible and near-infrared spectral regions, these microscopes are capable of examining fluorescence emission ranging from 400 to 750 nanometers. Download this review article to learn more.

Contributing Authors

Kenneth W. Dunn and Exing Wang - Department of Medicine, Indiana University, School of Medicine, 1120 South Drive, FH115, Indianapolis, Indiana 46202-5116.

John M. Murray - Department of Cell and Developmental Biology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, 19104.

Stephen W. Paddock, Eric J. Hazen, and Peter J. DeVries - Laboratory of Molecular Biology, Howard Hughes Medical Institute, University of Wisconsin, Madison, Wisconsin 53706.

James B. Pawley - Department of Zoology, 1117 W. Johnson Dr., University of Wisconsin, Madison, Wisconsin 53706.

David W. Piston - Department of Molecular Physiology and Biophysics, Vanderbilt University, 702 Light Hall, Nashville, Tennessee, 37212.

Kenneth R. Spring - Scientific Consultant, Lusby, Maryland, 20657.

Matthew J. Parry-Hill, Thomas J. Fellers, 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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