Sunday Short Courses
Sunday, July 31, 2022
- All short courses start at 8:30 AM and end by 5:30 PM.
- Separate registration fee required — see registration form.
- A certificate of attendance will be emailed to each participant.
- Mid morning and mid afternoon breaks are provided
- Breakfast and lunch are on your own
X-10 High-Resolution Structure Determination by Cryo-EM - Rescheduled for M&M 2023 - Minneapolis, MN
X-11 Explaining the New World Order of Biological Fluorescence Microscopy
University of South Carolina School of Medicine
- Basics of fluorescence
- Basics of confocal microscopy
- New fluorescence imaging modes
- Selection of appropriate imaging modes
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
Lawrence Berkeley National Laboratory
- Electron detector technology suitable for 4D-STEM experiments.
- List of possible 4D-STEM experimental configurations and references.
- Analysis software for characterizing large numbers of STEM diffraction pattern images and visualization of the results.
- Software and tutorial for simulating 4D-STEM datasets
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
Rocky Mountain Laboratories/NIAID/NIH
Jason de la Cruz
- Installation, calibration, and operating concept of SerialEM
- Image acquisition techniques such as for tilt-series, single-particle, and micro-ED
- Ancillary hardware such as direct-electron detectors, energy filters, and phase plates
- Scripting to extend SerialEM
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
Arizona State University
This course will introduce the fundamental concepts for in situ electron microscopy. It will include topic such as:
- Hot stages
- Gas cells
- Liquid cells
- Biasing holders
- Magnetic field
- Light illumination
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.â€¦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
Ismail El Baggari
Brookhaven National Laboratory
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
University of Manchester and SuperSTEM Laboratory, UK
National Institute of Standards and Technology, Boulder, US
- Introduction to HyperSpy and related Python libraries for multi-dimensional image and spectra processing and analysis.
- Curve fitting of multi-dimensional datasets.
- Machine learning.
- Big data analysis strategies.
- EELS and EDS analysis.
- Optional: application to the analysis of atomic resolution images, scanning electron diffraction and 4D STEM datasets.
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
Carnegie Institution for Science
NYU Langone's Microscopy Laboratory
Donald Danford Plant Science Center
- Basic biological EM sample processing, conventional workflow and basic reagents
- Particulate biological sample processing, agarose enrobing, negative staining
- Ultramicrotomy: Instrumentation, techniques and tips and tricks
- Special considerations for common biological EM specimen, specimen orientation, location of ROI, etc.
- Conventional biological EM sample processing for scanning electron microscope
- Rapid EM sample processing workflow, instrument assisted and automated sample processing and others
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.