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Scipion EM Classes

Electron microscopy image processing follows a common workflow. Protocols for the different image processing steps are represented below (click on image to see full size image).

General EM protocols hierarchy

Fig. 1. General EM protocols hierarchy

Data objects processed on these protocols are the following:

Electron microscopy data objects

Fig. 2. Electron microscopy data objects

Each package provides its own implementation of the different protocols, e.g.: Xmipp.

Xmipp EM protocols hierarchy

Fig. 3. Xmipp EM protocols hierarchy

Note: These diagrams were generated using pyreverse in the following way:

pyreverse -A -o png -p protocol pwem/protocol* --only-classnames
  • -A: looks for all ancestors in all classes

  • -o : specifies output format

  • -p: generates output files using project name provided

In this example we used `pwem/protocol*` as input to generate protocols hierarchy only.

If you get a “No such file or directory” error, you might need to install graphviz

`sudo apt-get install graphviz`