Accessibility disclaimer: To obtain information contained in document files on this page in an accessible format please contact the Electron Microscopy Center at (812) 856-1457 or through email at dagmorga@indiana.edu
Procedures, Protocols and Other Help
This page has a collection of procedures and protocols for various things such as sample preparation, using the various pieces of equipment and dealing with the computer side of things. Within the major categories shown below, the entries are listed alphabetically. A number of the pages here are also available through our Frequently Asked Questions (FAQ).
General Electron Microscopy
- General TEM Tutorial by John Rodenburg (recommended by former grad student Andrey Malyutin)
- Transmission Electron Microscopy (2nd ed.) - Chapters 1-10 by David B. Williams and C. Barry Carter (highly recommended as one of the most readable books on EM)
Sample preparation issues
- Buffers to use (and to avoid)
- Cryo-tomography Video (from Grant Jensen's lab)
- Deep stain embedding
- Glow discharging grids
- Negative staining
- Removing plastic from grids
Computer related items
- Dealing with image data on Karst
- Image processing tutorials with:
- auto3dem tutorial
- EMAN tutorial
- EMAN2 tutorial
- Relion tutorial
- SPARX tutorial
- Spider tutorial
- Xmipp tutorial
- Sending graphics from Karst to a Windows machine or a Mac
- Starting to use auto3dem
- Submitting jobs to the queue on Karst
Equipment usage
The links here connect to documents related to equipment in the EMC
- AFS 2 Freeze Substitution Robot
- Denton DV502 Carbon Evaporator
- JEOL JEM 1010
- JEOL JEM 1400plus
- JEOL JEM 3200FS
- Polaron E5100 Sputter Coater
- Vitrobot MK3
- Wohlwend High Pressure Freezer
Other useful information
- Documentation on our procedures
- Documentation on various commercial products
- Documentation on high pressure freezing and freeze substitution (HPF/FS)
Other documents
- Early history of Electron Micrscopy
- Atlas of Optical Transforms by G. Harburn, C.A. Taylor and T.R. Welberry
These entries are prepared as needed or requested, so please feel free to contact David Morgan at dagmorga@indiana.edu if you would like something added to this collection.