Main Page

Welcome to the Leschziner Lab's Tutorials Wiki

In these pages you will find tutorials designed to explain, in an accessible way, some of the principles behind the techniques used in our lab. They range from the very general (How does a microscope work?) to very specific approaches used in Three-Dimensional Electron Microscopy (3D-EM). This wiki is, by definition, a "work in progress"; we will periodically add new material and update what's already here. Blue links are for tutorials already available while red ones are for those we are still developing.

We hope you find the material useful and welcome feedback on how to improve it. To give us feedback, please see the discussion tab at the top of the page, or e-mail us.

Introduction

The compound optical microscope, first recognized in 1590, is probably the most familiar of all laboratory instruments, especially for biologists. The electron microscope, for many years simply an exotic rarity, has also become a standard tool in biological research. Both instruments are often used quite effectively with little knowledge of the relevant theory, or even how the particular microscope functions. Eventually, however, proper use, interpretation of images, and choices of specific application demand an understanding of fundamental principles.

This wiki is intended to provide both a brief overview of such concepts, as well as a more in-depth theoretical view for those readers who would like to examine more of the mathematics and physics behind imaging (such as with image formation, contrast, resolution limits). In particular, Fourier imaging will be discussed as it applies to the interpretation of data.

Since our focus is not directed toward crystalline data sets but rather what can be referred to as asymmetric structures, the image processing and data interpretation sections will deal with techniques particular to the latter.

General imaging principles

These conventions and basic physics concepts are fundamental tools for understanding electron imaging.

• Light optics
• Microscope Ray Tracing
• Phase Contrast
• Depth of Field

Electron imaging

There are many caveats to imaging with electrons as opposed to photons.

• What is an Electron Microscope?
• History of the Electron Microscope
• Types of Signals
• Electron optics
• The Weak-Phase Object Approximation
• Contrast
• Ewald Sphere
• Aberrations
• Special Imaging Techniques

Electron Microscopy of Macromolecules

• Sample Preparation
• Special Considerations

Three-dimensional reconstruction by EM

A "30 Second Overview" of three-dimensional EM reconstruction.

Basics

• Central Section Theorem
• Back Projection

Existing Reconstruction Methods

• Angular Reconstitution (AR)
• Random Conical Tilt (RCT)
• Orthogonal Tilt Reconstruction (OTR)

Software Available

An overview of the currently available software, links, and general descriptions.

Resolution

The concept of resolution in electron microscopy has brought out several debates in the past.

Hardware Innovations to the Electron Microscope

Some new, some old, there are many aspects of the microscope that may be changed, ostensibly altering the physics of image formation for the better.

• CMOS
• Phase Plates

---

Back to Leschziner Lab Main Site