Sunday Short Courses

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

LEAD INSTRUCTORS:
Tim Grant, Morgridge Institute / University of Wisconsin-Madison
Mike Cianfrocco, University of Michigan

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

LEAD INSTRUCTORS:
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

LEAD INSTRUCTORS:
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

LEAD INSTRUCTORS:
Cindi Schwartz, Rocky Mountain Laboratories/NIAID/National Institutes of Health
Guenter Resch, Nexperion, Austria
Jason de la Cruz, Memorial Sloan Kettering Cancer Center

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

LEAD INSTRUCTORS:
Robert Sinclair, Stanford University
Peter Crozier, Arizona State University

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 Data Analysis in Materials Science

LEAD INSTRUCTORS:
Eric Prestat, University of Manchester and SuperSTEM Laboratory, United Kingdom
Joshua Taillon, National Institute of Standards and Technology

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).