eTraining Introduction

Specimen Preparation

Leica Ultracut UCT



Hitachi S-4700 FE-SEM

Hitachi FB-2000A FIB


Veeco Dim 3000 AFM

Fluorescence Microscopes


More Resources


Basic Photoshop For Electron Microscopy

(Mostly) Simple Techniques to Tune-Up Your Electron Micrographs with Adobe Photoshop, authored by Eric Jay Miller, NUANCE Center, Northwestern University. This paper will discuss several simple procedures that can help to punch your micrographs up a notch. These instructions are written in such a way that just about anybody should be able to pick them and start using them without any previous experience with Photoshop.


Chloride Penetration Profile Determination with ESEM

This method utilizes the environmental scanning electron microscope and x-ray spectroscopy to determine the chlorine concentration at various depths within suitably prepared concrete specimens. The wiki is maintained by MiSTI, the US DOT University Transportation Center for Materials in Sustainable Transportation Infrastructure at Michigan Tech.

Concepts in Fluorescence Microscopy

Concepts in Fluorescence Microscopy

This website, maintained by Nikon, includes review articles, interactive Java tutorials, interactive Flash tutorials, digital image galleries, digital video galleries, and selected literature references.

Journal of Microscopy

Drying cells for SEM, AFM and TEM by hexamethyldisilazane: a study on hepatic endothelial cells.

This article is a reference for histology. Braet, F., DeZanger, R., and Wisse, E. (1996) "Drying cells for SEM, AFM and TEM by hexamethyldisilazane: a study on hepatic endothelial cells," Journal of Microscopy 186 (1). Pp. 84-87 Laboratory for Cell Biology and Histology, Brussels, Belgium.

Concepts in Fluorescence Microscopy

Education in Microscopy and Digital Imaging

The Carl Zeiss Microscopy Online Campus website explores the fascinating world of optical microscopy and provides the necessary background to understand both the basic concepts and advanced principles.

EDX Image Mode

EDX Image (X-ray Mapping) Mode

This procedure is for acquiring X-Ray maps. Detailed manufacturer's instructions can be found in the online in v 1.6.0 EDX Image Mode under 4pi Spectral Engine Resource Manual and Revolution User Guide in the support pages for 4pi Analysis, Inc.


EMAL: Electron Microbeam Analysis Laboratory - Microscopy Teaching & Learning Resources

The following tutorials, lectures, short courses, web course, etc. are offered by personnel in the field of microscopy from across the globe. Some are presented by people associated with the University of Michigan Electron Microbeam Analysis Laboratory, often as part of full fledged courses such as MSE-562.

Epoxy Resins

Epoxy Resins

The withdrawal (2007) of the Ciba-Geigy resin Araldite MY 778 and Hardener HY 951 from the market has forced the Facility to re-look at the most suitable epoxy resins to use for Secondary Ion Mass Spectrometry (SIMS) analysis. This specimen preparation site is maintained by the School of Geosciences Research Facility, Science and Engineering at The University of Edinburgh, for their Ion Microprobe Facility.

Light Microscopy

Fundamentals of Light Microscopy and Electronic Imaging

This text is a reference for the Zeiss AxioVert 200 M and ApoTome. Murphy, Douglas B. Fundamentals of Light Microscopy and Electronic Imaging. Wiley-Liss. Hoboken, NJ. 2001.



GeoPixelCounter is a Java-based program that can be used to estimate the the percentage of various minerals in a thin section of rock that has been digitally scanned into an image file. The program allows the user to click on a pixel in the image and then all other pixels that are close in color to the clicked-upon pixel will be changed to a new, easily visible color.

Comparative Physiology

A laboratory companion for General and comparative physiology

This text is a reference for histology. Hoar, William Stewart, and Cleveland P Hickman. A Laboratory Companion for General and Comparative Physiology. Englewood Cliffs, N.J.: Prentice-Hall, 1967.

Mineralogy Database

Mineralogy Database

The Mineralogy Database contains 4,714 individual mineral species descriptions with links and a comprehensive image library. The database also contains a birefringence chart example to determine thicknesses of thin samples.


Petrographic Methods of Examining Hardened Concrete: A Petrographic Manual

This is Publication No. FHWA-HRT-04-150, July 2006, by the US Department of Transportation Federal Highway Administration. See Chapter 5.3 THIN SECTIONS for much background information and procedural details on creating thin sections from flat samples.


Petrography of Igneous and Metamorphic Rocks

This text by Anthony R. Philpotts is a reference for thin section preparation. Published by University of Connecticut, Prentice Hall, Englewood Cliffs, New Jersey, 1989.

Carbon Film Thickness

The Role of Carbon Film Thickness in Electron Microprobe Analysis

This article is a reference for coating methods. D. M. Kerrick, et al, "The Role of Carbon Film Thickness in Electron Microprobe Analysis," The American Mineralogist, 1973, 58, 920-925.


Sample Preparation for Electron Probe Microanalysis—Pushing the Limits

This article concerns the critical nature of sample preparation to the analytical results of electron probe microanalysis. Geller and Engle are with Geller MicroAnalytical Laboratory, Topsfield, MA. Joseph D. Geller and Paul D. Engle, "Sample Preparation for Electron Probe Microanalysis—Pushing the Limits," Journal of Research of the National Institute of Standards and Technology, 2002, 107, 627-638.

SEM X Ray Analysis

Scanning Electron Microscopy and X-ray Microanalysis

This text is a reference for charging in the Hitachi S-4700 FE-SEM. Echlin, Patrick, and Dale E. Newbury. Scanning Electron Microscopy and X-Ray Microanalysis. 2nd ed. New York, NY: Springer, 1992. 111.

TEM Sample Preparation

Transmission Electron Microscopy (TEM): sample preparation guide

This site by CNRS (The National Centre for Scientific Research) provides guides to methodology, techniques, photo library, glossary, and books.

X Ray Generation Simulation

X-Ray Generation Simulation

This java based application by Electric Park Research simulates the generation of x-rays in the scanning electron microscope. The scanning electron microscope uses a beam of high energy electrons to illuminate the surface of a material.

External Websites

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