Sunday Short Courses

X10 - Exploring Cryo-Preparation Techniques for Biological Samples

Danielle Jorgens, University of California, Berkeley
Elizabeth Fischer, NIH NIAID Rocky Mountain Laboratories

In this short course, a variety of topics covering a spectrum of biological sample preparation needs will be reviewed, with special attention paid to cryo-preservation via high pressure freezing, plunge freezing, and cryosectioning. In addition, the course will focus on how to best prepare samples for the newest imaging tools and approaches in biological EM imaging, including correlative LM-EM, volume EM, cryo-SEM, and cryo-TEM. Tips and tricks on sample screening and sample-preparation artifacts will be covered. Participants will walk through the "ins and outs" of how to prepare samples for their specific experiments. After the course, participants will be provided access to a library of on-line reference material.

X11 - Advanced Focused Ion Beam Methods

Joseph Michael, Sandia National Laboratories
Lucille Giannuzzi, EXpress LO, LLC

The use of FIB instruments in materials- and biological-science laboratories is growing rapidly. The versatility and capabilities of these tools are also rapidly improving. This course will first cover ion/solid interactions, which are very important for a user of FIB instrumentation to understand. We will discuss different ion sources and the various ions that are now commercially available in FIB instruments, and explore their benefits for a range of applications. We will then discuss techniques of sample preparation for SEM and TEM, 3D applications, and micro- and nano-fabrication.

X12 - Practical Considerations for Image Analysis and ImageJ and Clemex Vision

James Grande, General Electric Global Research

This workshop covers a wide range of practical topics in the field of image analysis. Subjects will be covered in an easy-to-understand format so that users with little or no experience can understand how image analysis can provide extensive quantitative measurements that may lead to better understanding of material performance. Topics will range from input devices to image-processing algorithms and how best to extract quantitative data. Treating image analysis as a problem-solving tool along with discerning key metrics within a microstructure is discussed through several real-life examples. Comparisons using ImageJ/Fiji and a commercial image analysis product will be demonstrated.

X13 - SerialEM for EM Data Acquisition

David Mastronarde, University of Colorado, Bounder
Cindi Schwartz, NIH NIAID Rocky Mountain Laboratories
Guenter Resch, NIH NIAID Rocky Mountain Laboratories

The course is intended to be of interest to both beginners and advanced users of SerialEM in both biological- and materials-science disciplines. Developed by David Mastronarde at the University of Colorado, SerialEM is open-source and widely used in TEM data acquisition. It is unique in its adaptability for many imaging techniques. The instructors will explain installation and calibration of SerialEM, including use of direct-electron detectors and imaging energy filters, and will cover imaging techniques such as tilt-series acquisition, low-dose imaging, single-particle acquisition, montaging, mapping, and STEM. We will discuss advanced programming such as scripts (macros), plugins, and working with the navigator file or image data to extend SerialEM beyond its native capabilities. A demonstration specifically for course attendees will be performed in the exhibit hall.

X14 - Sample Preparation for High-resolution EM of Materials

Donovan Leonard, Oak Ridge National Laboratory

This course is intended for attendees using electron microscopy (e.g. SEM, STEM, TEM) to image samples at high magnification. Topics covered will consider minimization of preparation artifacts in order to achieve representative samples that yield high-quality micrographs. Methods producing consistent high-resolution SEM and atomic-resolution TEM/STEM imaging will be discussed.

X15 - Introduction to SEM with EDS: Imaging and Compositional Analysis

Keana Scott, National Institute of Standards and Technology
Nicholas Ritchie, National Institute of Standards and Technology

This introductory-level course will cover basic SEM instrument operation, imaging modes, and compositional analysis with an energy-dispersive x-ray spectrometer. We will approach the subject from the perspective of taking high-quality data that can be used to answer metrological, materials and compositional questions with a high degree of confidence. We will discuss practical considerations and strategies for different types of applications. The course will conclude with discussions of the latest SEM technologies, x-ray detector options, add-on tools, and image-analysis methods.

X16 - Multivariate Methods and Image-processing for Quantitative Microscopy

Stephen Jesse, Oak Ridge National Laboratory
Alex Belianinov, Oak Ridge National Laboratory
Suhas Somnath, Oak Ridge National Laboratory
Christopher R. Smith, Oak Ridge National Laboratory

Recent advances in microscopy hardware, statistical algorithms, and supporting information technology have made large volumes of high-veracity materials data easy to acquire. However, these hyperspectral data conceal pertinent information that is difficult to extract and interpret when the data size is large, complex, and corrupted by noise. In this tutorial, we will demonstrate a set of open-source Python-based tools that will make image- and spectral-data processing significantly easier for beginners and experts alike. We will showcase implementation, and highlight strengths and weaknesses, of various image-processing and machine-learning methods for a subset of real-world microscopy problems.


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