The Boulder Laboratory
For 3-D Electron Microscopy of Cells

Supported by

National Institutes of Health
National Institute of General Medical Sciences

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The Boulder Laboratory for 3D Electron Microscopy of Cells Department of MCD Biology
Campus Box 347
University of Colorado
Boulder, CO 80309


One of the laboratory's missions as a national resource facility is to disseminate information on techniques and software that have been developed and advanced here. Below are a list of documents containing instructions, strategies, and procedures for sample preparation and for the use of the software packages that have been developed for tomographic acquisition. The following links are to pdf documents.

Sample Preparation

The Boulder Laboratory for 3D Electron Microscopy developes techniques for preserving cellular structure with the highest degree of reliability. These techniques involve different methods for rapidly freezing samples in order to halt structural and biochemical activity in a very short timeframe, thus preserving structure in the "live" state.


Practical Methods in High-Pressure Freezing, Freeze-Substitution, Embedding and Immunoctocheminstry for Electron Microscopy

This manual is a technical guide to methods in high pressure freezing and subsequent freeze-substitution fixation and embedding for high resolution electron microscopy and EMimmunocytochemistry.

Software Documentation

Visit the IMOD, PEET, and SerialEM websites for complete documentation and software downloads. Below is a list of quick links to some of the information on these sites. Tutorial videos are also available on our YouTube channel.


IMOD User Guide

Introduction to 3DMOD

Tomography Guide

Guide to joining plastic serial section tomograms


SerialEM help documents

Introduction to SerialEM

A detailed introduction into the basic operations of Serial EM

Low dose, Navigator, Energy Filtering

Overview of low dose mode, using the navigator and energy filtering

Maps and Low Dose

How to set up medium and low magnification maps, and setting up low dose

Stategies for Cryo-Tomography Tilts Series Acquisition

Addresses the challanges inherent in cryo electron tomography image acquisition

Macros, Camera issues, Setting up the program

Using macros, camera issues, and setting up Serial EM

Optomizing Tomography for Plastic Sections

Special considerations for working with plastic embedded sections