Biology Department Biology Department  

Scanning Transmission Electron Microscopy Facility

Analyzing STEM Data

As STEM data is acquired we transfer it to our FTP server: and inform users via. e-mail. We generally provide some comments about overall quality, suggestions for analysis and current TMV calibration.

The following sections provide information on:

STEM Data Format
Downloading Images & Software
PCMass Manual
PCMass Tutorials

  1. Manual Mass Measurement
  2. Automatic measurement of a single image
  3. Customizing models and selection parameters
  4. Automatic measurement of a series of images
  5. Global statistics and accuracy
  6. Image averaging
  7. Filament analysis

Accuracy & Statistics

  The PCMass software includes a folder of practice images for use with the tutorials. We recommend the tutorials as a starting point before beginning analysis of your own data. The PCMass manual includes additional details about the internal operation of the software, but is not essential for normal analysis.


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Last Modified: June 12, 2009
Please forward all questions about this site to: Kathy Folkers

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