Concise introductory texts to the principles of electron microscopy and e-beam microanalysis:

Introduction to Scanning Electron Microscopy (SEM)
Introduction to Transmission Electron Microscopy (TEM)
Introduction to Energy Dispersive X-ray Spectroscopy (EDX) of bulk specimens
Introduction to Energy Dispersive X-ray Spectroscopy (EDX) of thin specimens
FEI introduction to electron microscopy
Introduction to EBSD
RISE Correlative Raman microscopy

Abbreviated operation manuals for some of the EMs in CFAMM:

SEM NNS450
SEM Quanta 200
FIB Quanta 200
SEM Mira3
Oxford Instr. Aztec

General guidelines for sample preparation for electron microscopy

Sample preparation for SEM
Sample preparation for EBSD

Oxford Instr. Aztec tutorial videos

Aztec user interface
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PointID EDS
EDS Map
EDS Quant
EBSD
Reporting