Giacovazzo - Fundamentals of Crystallography
Clearfield - Principles and Applications of Powder Diffraction
Waseda - X-ray Diffraction Crystallography
You can follow the book on "Transmission Electron Microscopy" written by "David Bernard Williams, C. Barry Carter" for the details of electron microscopy. For details of X-ray crystallography you can follow the above suggested books.
For SEM analysis: Lyman, Charles E., et al. Scanning electron microscopy, X-ray microanalysis, and analytical electron microscopy: a laboratory workbook. Springer Science & Business Media, 2012.
For XRD analysis: Waseda, Yoshio, Eiichiro Matsubara, and Kozo Shinoda. X-ray diffraction crystallography: introduction, examples and solved problems. Springer Science & Business Media, 2011.
For EDX analysis: Russ, John C. Fundamentals of Energy Dispersive X-Ray Analysis: Butterworths Monographs in Materials. Butterworth-Heinemann, 2013.
Start with a classic one of
Joseph Goldstein: https://www.amazon.com/Scanning-Electron-Microscopy-X-ray-Microanalysis-ebook/dp/B000VQEY5K
There you will find answers to 99.99% of your questions about EM-techniques.
There are several great journal articles available on the topics but are you able to give more details on your project? By providing this information we all can provide you with better articles that pertain more to your research. Are you trying to use these methods to evaluate the same materials/project or for different projects?
For XRD and crystal structure understanding, this two books are very helpful:
Elements of X-Ray Diffraction by Bernard Dennis Cullity,
The crystal structure of solids by P. J. Brown.
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