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short courses



These half- or full-day workshops occur throughout the SciX conference and are open to conference and non-conference attendees for a separate registration fee.  Stay tuned for registration opening.

Half day conferee: $225
Half day non-conferee: $325
Half day student: $25
Full day conferee: $450
Full day non-conferee: $550
Full day student: $50


Sunday, October 13, 2019


9:00am – 12:00pm A Practical Introduction to Infrared, Raman,and Near Infrared Spectroscopy

James A. de Haseth, University  of Georgia                                                        

This course will present the origins of spectral bands in Infrared, Raman, and NIR spectroscopy. This will start with a discussion of the fundamental vibrations in mid-infrared and Raman spectra and explain how overtone and combination bands can appear in the NIR as well as in mid-infrared and Raman spectra. Some direct guidelines will be presented to show which transitions are allowed. This will not be a theoretical discussion that involves mathematics or quantum mechanics, but rather an understanding of the physical phenomena that led to the development of the mathematical approaches. Further topics include instrumental issues such as resolution, instrumental effects on spectral lineshape, and effects of mathematical manipulation of spectra.               



9:00 am – 4:00 pm Basic Chemometrics      

Barry Wise, Eigenvector

This course concentrates on what are perhaps the two most important chemometric methods, Principal Components Analysis (PCA) and Partial Least Square (PLS) regression. PCA can be used for exploratory data analysis, pattern recognition and data prescreening/cleaning. PCA is part of many other methods and is also used for preprocessing data in a wide variety of applications (e.g. SVMs and ANNs). This course covers the basics of PCA, concentrating on interpretation of PCA models. The course continues with the motivation regression models. Multiple Linear Regression (MLR) is introduced along with Principal Components Regression (PCR). Problems with these methods are discussed, and it is shown how Partial Least Squares (PLS) mitigates these issues. Examples of using PLS in spectroscopic calibrations is demonstrated. The course includes hands-on computer time for participants to work example problems using PLS_Toolbox.


1:00 pm – 4:00pm Searching Infrared and Raman Spectra 

James A. de Haseth, University of Georgia                                                                         

In a general sense, spectral searching is a simple operation. An unknown spectrum is presented to the search system software, the spectral databases are searched, and a result presented. This simple operation in no way explains how to optimize the process to arrive at the best, ideally the correct, identification. There is more than one search algorithm, so which one should be used?  What if the unknown compound is not in the database?  What if the unknown spectrum represents a mixture?  How can we proceed to find these answers?  This course will address these issues and more.

Participants will be provided with a two-week trial copy of Bio-Rad Informatics KnowItAll® Software to use during and after the course. It will not be possible to provide laptop computers for participants; therefore, the software will be sent to the participants shortly before the course so that it can be installed on a Windows 7 or 10 laptop computer.

Monday, October 14, 2019


9:00 am – 12:00 pm Introduction to Hyperspectral/Multivariate Image Analysis       

Robert T. Roginski, Eigenvector 


Hyperspectral images are becoming increasingly common in analytical chemistry and remote sensing applications. They are based on several types of spectroscopy and spectrometry including Raman, IR and SIMS. Introduction to Hyperspectral/Multivariate Image Analysis starts with a brief review of sources of multivariate images and tools for viewing and investigating them. Particle analysis is then considered, followed by texture analysis. Practical image analysis with Principal Components Analysis (PCA) demonstrates how information from hyperspectral images can be compressed and displayed, and how classification tools can be used to identify similar areas. The course concludes with some examples of Multivariate Curve Resolution (MCR) on images and demonstrates how it can be used to create chemical maps. The course includes hands-on computer time for participants to work example problems using PLS_Toolbox and MIA_Toolbox or Solo+MIA.      


9:00 am – 12:00 pm Intro to Raman with Imaging Applications          

David Tuschel, LBT Scientific Consulting 

In this course, you will learn the basics of applied Raman spectroscopy and imaging. In addition, students will be taught the application of group theory to crystalline materials and how to apply those symmetry rules to perform “Raman Crystallography”. The topics and content will be of value to researchers in industry and academia, analytical chemists, laboratory technicians, teachers, graduate students and materials scientists. The instructor will teach Raman spectroscopy and imaging at a practical level and cover those topics which will allow the student to apply the material learned in the laboratory, workplace and classroom. Students will learn about:

  • Raman spectroscopy through the classical description
  • The design of a Raman spectrometer and how each component affects the spectrum
  • Spatial resolution and confocality
  • The effect of microscope objectives on the Raman spectrum
  • Raman imaging including 3D imaging
  • Phonons and lattice vibrational modes
  • Low-Energy phonon modes
  • Chemical bond interactions and Raman band shape
  • Group theory and spectral selection rules
  • Crystal classes and Raman tensors
  • Polarization-Orientation micro-Raman spectroscopy
  • Application of “Raman crystallography”
  • Raman spectroscopy and imaging of few-layer 2D crystals


1:00 pm - 4:00 pm Non-Linear Methods for Regression and Classification  

Donal O’Sullivan, Eigenvector


While linear methods, such as PLS regression, work in a very wide range of problems of chemical interest, there are times when the relationships between variables are complex and require non-linear modeling methods. Many non-linear methods have been developed, however, we will focus on a few that we have found quite useful. The course begins with a discussion of linearizing transforms. Augmenting with non-linear transforms, e.g. polynomials, is discussed next. Locally Weighted Regression (LWR), Artificial Neural Networks (ANNs) and Support Vector Machines (SVMs) are then considered, with SVMS for both regression and classification considered. The course includes hands-on computer time for participants to work example problems using PLS_Toolbox and MATLAB on their own computers.                        

1:00 pm - 4:00 pm Problems with FT-IR Spectra and How to Avoid Them

Ellen Miseo, TeakOrigin

Jenni Briggs, Pike Technologies 

Gloria Story, Procter & Gamble

Users of FT-IR spectrometers may have received little or no formal training in spectroscopy and therefore cannot distinguish between “good” and “bad” spectra. In this course, we will show many of the problems that are commonly encountered with FT-IR spectra measured by inexperienced (and often experienced!) users and show how to avoid them. Problems can appear from the instrument, the sample accessory and/or presentation. Since the bulk of the samples that are currently analyzed are done by Attenuated Total Reflection we will cover it in detail. We will also address common problems associated with other accessories. This year we will also be including a “tricks of the trade” component to the class.

Tuesday, October 14, 2019

9:00 am – 12:00 pm Laser Fundamentals for Spectroscopy   

Robert Chimenti, RVC Photonis/Rowan University                                                               

This course is designed to give attendees an introduction to the fundamentals of laser physics as well as a practical understanding of common laser designs and their applications in spectroscopy.  This course will begin by providing a fundamental understanding of the three basic components of a laser: gain medium, resonator, and excitation source. You will learn how these components affect the laser characteristics that are important to spectroscopists, specifically, mode structure, spectral linewidth, pulse-width and average power. Finally, attendees will be introduced to the pros and cons of common gas, solid-state, and diode laser designs as they apply to various spectroscopy applications.                

1:00 pm – 4:00 pm Portable Raman: What It Takes to Create Small Systems and What They Can Do for You       

Katherine Bakeev, B&W Tek       

Adam J. Hopkins, Metrohm                                                                      

1:00 pm – 4:00 pm Advance Applications of LAICPOES, LAICPMS and LIBS   

Jhanis Gonzalez, Applied Spectra / Lawrence Berkeley National Laboratory           


In recent years, both laser ablation sampling technologies (LA-ICP-MS/OES & LIBS) has established themselves as one of the most influential analytical techniques available in the marketplace. The reason for this success comes from their well-known advantages that include direct analysis of any sample, little to no sample preparation, rapid analysis time, and capability for obtaining spatial information (lateral and depth). The combination of these two techniques for simultaneous collection of Optical Emission data (LIBS and LA-ICP-OES) and Isotopic information (LA-ICP-MS) was reintroduced and gained popularity in the last few years with tremendous success. The success is attributed to complementary information provided by both techniques for elements that are separately unattainable due to low sensitivity, undetectability, and/or strong interferences. In this presentation, we examine insight on this combined approach and its impact on the analytical market for solid sample analysis.
 Wednesday, October 15, 2019

9:00 am – 12:00 pm Molecular Networking and The Global Natural Products Social Molecular Networking (GNPS) Platform for The Analysis of Metabolomics Data

  Amina Bouslimani, University of California San Diego

Alan Jarmusch, University of California San Diego

Mingxun Wang, University of California San Diego

This workshop will introduce ‘Molecular Networking’ tool to organize, visualize and analyses tandem mass spectrometry (MS/MS) data. Molecular networking compares, aligns and groups MS/MS spectra collected from different types of samples to highlight molecular families of structurally related compounds. Through molecular networking, MS/MS spectra are also annotated using spectral matching with reference MS/MS spectra from public databases. During this workshop, we will present the key steps required to generate a molecular network in the GNPS platform (http://gnps.ucsd.edu, Global Natural Products Social Molecular networking). You will learn how to create, visualize and analyze a molecular network generated from MS/MS data and how to use the ‘Library Search’ tool to annotate MS/MS spectra. Example data files from a forensic metabolomics study will be provided and we also encourage participants to use their own data. Finally, we will cover additional tools available on the GNPS platform such as the Molecular Blast (MASST) to search an MS/MS spectrum across all public datasets in GNPS, the feature based molecular networking that integrates OpenMS, MZmine2, MS-DIAL, XC-MS and MetaboScape, with GNPS, and other tools to analyze MS/MS data.



9:00 am – 4:00 pm Process Analytical Technology: Out of the Lab and into the Line

Jim Rydzak, Specere Consulting                


Process analytical technology (PAT) is a tool for product development, scale up and manufacturing of any chemical product. In this course, you will learn about the benefits of in-process monitoring, how to justify and plan the analysis implementation. Different process analytical tools will be discussed, how to implement them and how to choose between them for your application. How to use PAT to save time and money, improve your green scores in development and manufacturing become proficient at PAT will be discussed. Various applications, from various industries will be used to explain concepts and provide examples of implementation. 

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