Sunday Short Courses

Sunday, July 31, 2022

X-10 High-Resolution Structure Determination by Cryo-EM

Tim Grant
Morgridge Institute / University of Wisconsin-Madison

This one-day course will provide an overview of the theory and steps required for high resolution structure determination by single-particle cryo-EM, with a particular focus on image processing. The course will begin with lectures providing an introduction to the theory and methods relevant to specimen preparation, data collection and image-processing of the data. This will be followed by an interactive single-particle processing session and live processing of a dataset to high resolution using the cisTEM software package.

X-11 Explaining the New World Order of Biological Fluorescence Microscopy

Bob Price
University of South Carolina School of Medicine

Jay Jerome
Vanderbilt University

Fluorescence microscopy is a primary method for visualizing structure in three dimensions. Since our Basic Confocal Microscopy short course more than 10 years ago, tremendous advances in hardware and software have been made that have led to improved imaging depth/3D reconstruction technology and super-resolution imaging techniques such as PALM, STORM, SIM and several variations of these. We will review the basic principles of fluorescence and confocal imaging, provide information on how these principles relate to several new modes of fluorescence imaging, and discuss/compare how these new imaging modes have improved our understanding of fluorescence applications in biological/biomedical research.

X-12 Guidelines for Performing 4D-STEM Characterization from the Atomic to >Micrometer Scales: Experimental Considerations, Data Analysis and Simulation

David Muller
Cornell University

Colin Ophus
Lawrence Berkeley National Laboratory

With modern electron detector technology, it is now possible to record full images of a converged STEM probe while scanning it over the sample surface, resulting in a 4D-STEM dataset. Because the atomic-scale scattering information contained in an atomic-scale STEM probe is decoupled from the step size between STEM probe positions, 4D-STEM can be used for experiments ranging from sub-Angstrom resolution phase contrast imaging to statistical characterization of functional materials over large length scales. In this course, we will give tutorials on how to perform 4D-STEM experiments, analyze the (potentially very large!) resulting datasets, and perform 4D-STEM simulations.

X-13 SerialEM for EM Data Acquisition

Cindi Schwartz
Rocky Mountain Laboratories/NIAID/NIH

Guenter Resch
Nexperion, Vienna, Austria

Developed by David Mastronarde at the University of Colorado, SerialEM is open-source and widely used in automated TEM data acquisition on a multitude of microscope platforms and detectors. The course will be of interest to both beginners and advanced users in both biological and materials sciences. Installation and calibration of SerialEM will include use of direct-electron detectors and imaging energy filters. Imaging techniques such as tilt-series acquisition, low-dose imaging, single-particle acquisition, montaging, and mapping, as well as use of scripts (macros) and working with the navigator file or image data to extend SerialEM beyond its native capabilities will be covered.

X-14 In situ and Operando Approaches to TEM

Robert Sinclair
Stanford University

Peter Crozier
Arizona State University

This course will introduce the fundamental concepts for in situ electron microscopy. It will include topic such as:

In situ and operando transmission electron microscopy are becoming increasingly important in advanced materials characterization. Being able to observe materials in state that are similar to real world applications is now recognize as vital for relating structure to functionality. The ability to perform atomic level analysis while the sample is exposed to different stimuli/environments such as heat, strain, gas, liquids, electric field, magnetic field, light, etc.…is a key part of the in-situ approach. Operando approach require simultaneous measurement of some technologically relevant functionality such as current flow, deformation or catalysis.

X-15 Cryo-STEM and EELS for Materials Sciences

Lead Instructors
Ismail El Baggari
Harvard University

Myung-Geun Han
Brookhaven National Laboratory

Michael Zachman
Oak Ridge National Laboratory

While cryogenic TEM has revolutionized the research in biological science, its applications in materials sciences have been relatively limited. The major challenges lie in realizing reliable cryogenic specimen preparation, and atomic-scale imaging and spectroscopy at a wide range of cryogenic temperatures. Though still in its infancy, recent advancements in cryo-EM, especially in cryo-FIB and new TEM stages, have brought us the promises.

This short course will focus on the fundamentals of cryo-EM and primarily benefit those new to the field. We will highlight historical developments, current state, and future perspectives of cryo-EM for materials science. We will cover critical steps involved in a successful cryogenic microscopy study, including specimen preparation, specimen transfer, cryogenic FIB, new cryo-TEM stages, imaging, spectroscopy at low temperatures, and data analysis methods that can potentially be used to assist cryo-EM data acquisition and data analysis.

X-16 Data Analysis in Materials Science

Eric Prestat
University of Manchester and SuperSTEM Laboratory, UK

Joshua Taillon
National Institute of Standards and Technology, Boulder, US

This short course will introduce the use of HyperSpy and related Python libraries (atomap, pixStem, pyXem) for analysis of microscopy datasets. No prior Python knowledge is required. Attendees will learn how to perform basic machine learning, multi-dimensional curve fitting for EELS and EDS quantification, atomic resolution image analysis and big data processing (such as 4D STEM) on desktop computers. For this hands-on and interactive short course, attendees will need to install software on their own laptop in advance and bring it with them to the short course (instructions will be provided).

X-17 Biological EM Sample Processing

Lead Instructors
Ru-ching Hsia
Carnegie Institution for Science

Alice Liang
NYU Langone's Microscopy Laboratory

Kirk Czymmek
Donald Danford Plant Science Center

This course is the first installment of a two-part series of biology EM courses designed to introduce the principles and workflow of EM sample processing for animal and plant tissues, cultured cells, microorganisms and other particulate specimens. Participants do not need to have prior EM sample processing experience. The second installment (Part 2) of this course will be offered in 2023 and will include more advanced EM sample processing techniques.