Transmission Electron Microscopy

This course is part of the programme
Doctoral study programme Materials

Objectives and competences

The primary goal of the course is to provide students with the basic knowledge in the fields of transmission electron microscopy and microanalysis and based on the examples show the exceptional capabilities of techniques associated with this microscopy. In understanding and development of new materials with the tailored properties, knowledge of the structure and chemical composition at the atomic level is of key importance. Most macroscopic properties can be explained by the structure at the atomic level.
Students acquire basic knowledge, experience and competences for designing experiments in
Predvideni študijski rezultati:
Intended learning outcomes:
the transmission electron microscope and for evaluation and interpretation of the results.




  • Electron – solid interactions
  • Conventional transmission electron
    microscopy (CTEM – instrumentation, types of contrast, bright and dark field experiments, TEM sample preparation)
  • Electron diffraction (analysis of electron diffraction patterns, indexing, zone axis determination, crystallographic relationships)
  • High-resolution transmission electron microscopy (HRTEM – contrast transfer function, basics of phase contrast, influence of the thickness, through-focus series)
  • Scanning-transmission electron microscopy (STEM – detector types and information collected with different detectors and techniques)
  • Cs-corrected STEM microscopy, sub- Ångstrem resolution
  • Quantitative STEM microscopy on atomic level (determination of atom column positions and intensities)
  • HRTEM and STEM images simulations (modelling structures, calculation of HRTEM, HAADF and ABF images using multi-slice frozen-phonon method)
  • Energy-dispersive X-ray spectroscopy (EDXS) in TEM/STEM (elemental quali, quantitative analysis, elemental distribution, mapping)
  • Electron energy-loss spectroscopy (EELS) (chemical composition, valence state, coordination, mapping, sample thickness determination)
  • TEM/STEM tomography (3D structure determination)
  • In-situ techniques (heating, cooling, electrical and electrochemical measurements in TEM/STEM)
  • Typical examples of TEM and STEM techniques used in the determination of crystal structure, defects in the crystal structure and chemical composition on atomic level

Intended learning outcomes

Students learn about the basic principles of operation, instrumentation and the use of (scanning) transmission electron microscopy, Energy-dispersive X-ray spectroscopy and Electron energy-loss spectroscopy. They learn how to properly prepare samples and determine experimental conditions, how to design experiments inside the microscope, and how to select appropriate techniques. In the individual work under the supervision of the lecturer, they learn the basics of centering and tuning the microscope and collecting data (images, depiction images, spectra, etc.).
They learn to independently evaluate the results obtained and interpret them correctly. All these skills will enable them to select the methods of investigation in the future development or research work in science or industry and to analyse the results accordingly.


• Jingyue Liu, Advances and Applications of Atomic-Resolution Scanning Transmission Electron Microscopy, Microscopy and Microanalysis , Volume 27 , Issue 5 , October 2021 , pp. 943 – 995, Cambridge University Press, August 2021 E-version
• Karel Hendrik Wouter van den Bos, Thomas Altantzis, Annick De Backer, Sandra Van Aert & Sara Bals (2018) Recent breakthroughs in scanning transmissionelectron microscopy of small species, Advances in Physics: X, 3:1, 1480420 E-version
• C. Barry Carter and David B. Williams, Transmission Electron Microscopy, Diffraction, Imaging, and Spectrometry, 2016, Springer International Publishing Switzerland, eBook ISBN 978-3-319-26651-0
• Stephen J. Pennycook and Peter D. Nellist, Scanning Transmission Electron Microscopy, Imaging and Analysis, 2011, Springer-Verlag New York, eBook ISBN 978-1-4419-7200-2 E-version
• R.F. Egerton, Electron Energy-Loss Spectroscopy in the Electron Microscope, 2011, Springer US, eBook ISBN 978-1-4419-9583-4 E-version
• Christoph Koch, Determination of core structure periodicity and point defect density along dislocations, ProQuest Dissertations And Theses; Thesis (Ph.D.), Arizona State University, 2002, Publication Number: AAI3042580, ISBN: 9780493562612 E-version
• Vesta - program za modeliranje kristalnih struktur. E-version
• QSTEM - programi za simulacijo STEM slik. E-version
• Interaktivni portal za elektronsko mikroskopijo. E-version


40/60, Individual project assignments on different topics, which the candidate presents in a discussion with the lecturer. A final project connected with research work and presented by the candidate orally to other students.

Lecturer's references

Prof. dr. Goran Dražić (h=29) is heading an Electron microscopy and catalysis group at the Department for Materials Chemistry at National Institute of Chemistry, Ljubljana, Slovenia. He is a full professor at the Jožef Stefan International Postgraduate School where he is lecturing from 2005 in the fields of Transmission Electron Microscopy. He obtained his PhD degree in Chemistry from University of Ljubljana, Faculty for Chemistry and Chemical technology in 1990. As a postdoc he studied SiC hot corrosion at Forschungscentrum Jülich in Germany. Main areas of his research are the development and application of scanning transmission electron microscopy and spectroscopies at atomic level for the study of modern inorganic materials and the research and development of catalyst materials for photocatalysis and oxygen reduction reaction (fuel cells). His bibliography contains more than 210 scientific papers published in international peer-review journals, around 40 invited lectures and 10 book chapters. He was awarded with the Zois recognition for important scientific achievements in the field of Electron microscopy in 2000.

Selected publications:
1. MEHMOOD, Asad, GONG, Mengjun, JAOUEN, Frédéric, ROY, Aaron, ZITOLO, Andrea, KHAN, Anastassiya, SOUGRATI, Moulay Tahar, PRIMBS, Mathias, MARTINEZ BONASTRE, Alex, FONGALLAND, Dash, DRAŽIĆ, Goran, STRASSER, Peter, KUCERNAK, Anthony. High loading of single atomic iron sites in Fe–NC oxygen reduction catalysts for proton exchange membrane fuel cells. Nature Catalysis, Apr. 2022, vol. 5, iss. 4, str. 311-323, ISSN 2520-1158. doi: 10.1038/s41929-022-00772-9, IF = 41,8

  1. BENČAN, Andreja, OVEISI, Emad, HASHEMIZADEH, Sina, VEERAPANDIYAN, Vignaswaran K., HOSHINA, Takuya, ROJAC, Tadej, DELUCA, Marco, DRAŽIĆ, Goran, DAMJANOVIĆ, Dragan. Atomic scale symmetry and polar nanoclusters in the paraelectric phase of ferroelectric materials. Nature communications, ISSN 2041-1723, 2021, vol. 9, doi: 10.1038/s41467-021-23600-3, IF = 14,9

  2. LI, Jingkun, SOUGRATI, Moulay Tahar, ZITOLO, Andrea, ABLETT, James M., OĞUZ, Ismail Can, MINEVA, Tzonka, MATANOVIC, Ivana, ATANASSOV, Plamen, HUANG, Ying, ZENYUK, Iryna, CICCO, Andrea Di, KUMAR, Kavita, DUBAU, Laetitia, MAILLARD, Frédéric, DRAŽIĆ, Goran, JAOUEN, Frédéric. Identification of durable and non-durable FeNxFeNx sites in Fe-N-C materials for proton exchange membrane fuel cells. Nature Catalysis, ISSN 2520-1158, Published 07 December 2020, doi: 10.1038/s41929-020-00545-2, IF = 41,8

  3. CHOI, Chang Hyuck, LIM, Hyung-Kyu, CHUNG, Min Wook, CHON, Gajeon, SAHRAIE, Nastaran Ranjbar, ALTIN, Abdulrahman, SOUGRATI, Moulay Tahar, STIEVANO, Lorenzo, OH, Hyun Seok, PARK, Eun Soo, LUO, Fang, STRASSER, Peter, DRAŽIĆ, Goran, MAYRHOFER, Karl, KIM, Hyungjun, JAOUEN, Frédéric. The Achilles' heel of iron-based catalysts during oxygen reduction in an acidic medium. Energy & environmental science, ISSN 1754-5706, 2018, vol. 11, iss. 11, p. 3176-3182. doi: 10.1039/C8EE01855C, IF = 33,3

  4. ROJAC, Tadej, BENČAN, Andreja, DRAŽIĆ, Goran, SAKAMOTO, Naonori, URŠIČ NEMEVŠEK, Hana, JANČAR, Boštjan, TAVČAR, Gašper, MAKAROVIČ, Maja, WALKER, Julian, MALIČ, Barbara, DAMJANOVIĆ, Dragan. Domain-wall conduction in ferroelectric BiFeO3 controlled by accumulation of charged defects. Nature materials, ISSN 1476-1122, 2017, vol. 16, no. 3, p. 322-327, doi: 10.1038/nmat4799, IF = 39,2