Resources

External Resources on Microscopy

Microscopy is a large and ever expanding subject including optical theory, experimental practice, and a variety of specialized systems and techniques, often their own jargon, acronyms, and technical terms. We hope that the selection of resources listed below will provide you a starting point for better understanding the instruments in our laboratory and how you can use them better.

General Microscopy

Molecular Expressions: This site is dedicated to exploring the world of optical microscopy, including a large collection of photomicrographs as well as numerous links to other resources, including their Optical Microscopy Primer. The site is hosted and developed by a group at Florida State University, who also co-developed separate sites with other companies that provide more vendor-specific content including:

Microscope Hardware

Introduction to Microscope Objectives (Nikon MicroscopyU): This page describes the difference between achromatic, semi-apochromatic, and apochromatic objective lens and also describes how water and oil immersion objectives are constructed.
Resolution (Nikon MicroscopyU): This page explain the relationship between the resolution of an image and numerical aperture and magnification of an objective lens.
Numerical Aperture (Nikon MicroscopyU): This page defines numerical aperture and explains how the parameter is used to characterize microscope objectives.
The Nikon Perfect Focus System (Nikon MicroscopyU): This page describes how the Nikon Perfect Focus System uses an infrared laser beam to maintain a stable vertical focus on a specimen.

Brightfield Microscopy

Specimen Contrast in Optical Microscopy (Nikon MicroscopyU): This page provides an overview of the physical mechanisms and techniques used to create contrast in photomicrographs.
Introduction to Phase Contrast Microscopy (Nikon MicroscopyU): This site how phase contrast imaging is used to increase contrast for nearly transparent specimens like unstained cells.
Dark Field and Phase Contrast Microscopes (Quantum Made Simple): This video demonstrates the related techniques of dark field and phase contrast microscopes.
Differential Interference Contrast (Nikon MicroscopyU): This site links to several pages that describe how DIC is used to increase contrast for nearly transparent specimens like unstained cells, as an alternative to phase-contrast methods.

Epifluorescence Microscopy

Fluorescence Microscopy (Nikon MicroscopyU): This page links to a variety of other pages describing techniques of fluorescence imaging. To start, the tutorial Introduction to Fluorescence Microscopy describes how epifluorescence microscopy is implemented in practice along with the advantages and disadvantages of the method.
Fluorescence Microscopy Techniques - Which is Best for Me? (Addgene): This page summarizes many of the techniques used in fluorescence imaging and describes the types of situations that would be best suited for each (e.g. static vs. dynamic, thick vs thin).

Confocal Laser Scanning Microscopy

Confocal Microscopy (Nikon MicroscopyU): This page links to a variety of other pages describing the concepts and techniques of confocal imaging including
- Introductory Confocal Concepts: This page describes the concepts and hardware needed for confocal microscopy.
- Confocal Imaging Modes: This page explains techniques including optical section, time-lapse, Z-series (3D), 4D, and X-Z imaging.
- Spectral Imaging and Linear Unmixing: This page describes how spectral detection units can be used to separate signals from dyes with closely-space emission peaks.
Flourescent and Confocal Microscope (Quantum Made Simple): This video illustrates the principles of fluorescence and confocal microscopes.

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