7 tutorials for users will be held on February 8:


MX-BAG Meeting
PyMca
EXAFS and FDMNES
Coherence reconstruction Software - Roundtable Discussion
Volume image analysis of tomographic data
SAXS data reduction and analysis
Electronic structure and lattice dynamics calculations in complex systems
 

Organisation of the tutorials:

The number of participants per tutorial is limited (except for the tutorials "Coherence reconstruction software" and "EXAFS + FDMNES, morning session)) and you must attend the full session of the tutorial(s) you sign up for: so please select carefuly the tutorial(s) you would like to attend, register your participation via the registration form and do not forget to modify your registration form if you change your mind to give the possibility to other scientists to register. Please note that due to the timings of the different tutorials, it is not always possible to register for more than one tutorial, therefore please check the schedule of the Tutorials you are interested in before signing up!

 

MX-BAG Meeting

Organiser: Gordon Leonard, ESRF, contact
Monday 8 February: 8h30 - 18h30

Scope

A meeting of ESRF BAG Responsibles (by invitation only) that includes presentation of the facilities for Structural Biology at ESRF, visits to the new end-stations available for Stuctural Biology and a round table discussion concerning the future of Structural Biology Facilities at ESRF.

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PyMca

Organiser: Armando Sole, ESRF, contact
Monday 8 February: 9h00 - 18h30

Scope

The aim of this tutorial is to train the attendants on the use of PyMca for X-Ray Fluorescence Analysis (XRF) and for Imaging. The tutorial goes from XRF basics to full quantitative analysis.

The participants will learn to calibrate spectra, to identify peaks, to model experimental setups, to perform quantitative analysis and to process large sets of data. The imaging capabilities of the program and the possibilities offered in other fields than XRF, like mapping experiments using x-ray absorption spectroscopy or combining XRF and Powder Diffraction, will also be presented.

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EXAFS and FDMNES

Organiser: Sakura Pascarelli, ESRF, contact

Morning session (9h00 - 12h30): Introduction to XAS and EXAFS (all participants)
Afternoon session (14h00 - 18h00): Parallel sessions

Please use these links to upload the slides of the tutorials:

Scope

Introduction to XAS and EXAFS

This tutorial provides a very general introduction to the fundamentals of X-ray absorption spectroscopy. The orign of the Extended X-ray Absorption Fine Structure (EXAFS) will be explained first using hand waving arguments. A simple theoretical description of this quantum mechanical phenomenom will then be given and the EXAFS equation will be derived in a more formal manner starting from Fermi's golden rule for the transition probability. A simple introduction to XAS data analysis will be given: extraction of quantitative values for local structural parameters (near neighbor ditances, coordinatin numbers, and atomic species) from the EXAFS and information on formal valence and coordination chemistry from the XANES. Finally, a few samples of applications will be given, starting from major historical EXAFS breadthroughs to a selection of recent results at the ESRF.

Parallel sessions

  • EXAFS data analysis (maximum of 8 participants)

The basic steps of EXAFS data analysis will be shown "hands-on", starting with the extraction of the EXAFS signal from the measured absorption spectrum to the quantitative fitting of the first coordination shells. We will use the Athena and Artemis software packages. The tutorial will be split into two sessions: a common session, where we all analyze the same data set together, and individual sessions where each participant will be able to do data  analysis exercises with available data or with their own data.

  • FDMNES theory and applications (maximum of 8 participants)

FDMNES performs calculations of XANES, DAFS, XRD and XRS using fully relativistic monoelectronic calculations (DFT - LSDA). It uses the Finite Difference Method (FDM) to solve the Schroedinger equation, and the shape of the potential is free (non- Muffin tin approximation). This 3 hour-tutorial will introduce the theoretical frameword of the FDMNES approach, and will provide an opportunity for hands-on practice of data analysis.

Note: participants of this session should bring their personal laptop (Windows or Linux) but no MAC.

  • EXAFS practical on beamlines BM25 and BM20 (maximum of 4 participants per beamline)

The goal of this practical is to show the experimental requirements necessary to record X-ray absorption (EXAFS / XANES) spectra. Three aspects will receive special attention: i) Beamline optics setting and alignments, ii) sample prepartion and iii) detection / acquisition modes. After a short presentation of the beamline setup, different aspects of the EXAFS experimental set-up will be discussed. Two different types of samples will be studied which require different experimental setups: transmission and fluorescence modes.

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Coherence reconstruction sofware - Roundtable Discussion

Organiser: Tobias Schulli, ESRF, contact
Monday 8 February: 16h30 - 18h30

Scope

Methods exploiting the coherence of the X-ray beam have gained significant importance and are rapidly gaining ground as a new and unique imaging tool. Coherent diffraction imaging and ptychography in both forward scattering and under Bragg condition suffers from a lack of widely available, documented and maintained "easy to use" software. Although numerous expert groups have worked on their own solutions, to open such techniques to the non-expert user community a coordinated effort is required. The aim is to develop an open access transparent toolkit to support the growing user community in this field.

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Volume image analysis of tomographic data

Organiser: Alexander Rack, contact
Monday 8 February: 14h00 - 18h00

Scope

Imaging methods using penetrating radiation provide insight into heterogeneous materials or engineering components. In combination with (micro)tomography they yield a fully three-dimensional representation of the object (micro)structure. Both computed tomography with high spatial resolution and quantitative volume image analysis have made enormous progress. In particular for materials and natural science applications the combination of high-resolution three-dimensional imaging and the subsequent image analysis exploiting the fully preserved spatial structural information yield new and exciting insights.

In this tutorial, field-tested and up-to-date methods for quantitatively analysing three-dimensional images are introduced. By selected applications  the use of volume image analysis will be outlined: it allows for determination of spatial cross-correlations between different constituents of a specimen, investigation of orientations or derivation of statistically relevant information such as object size distributions. The core part of this work consists, besides the exemple application scenarios, in the processing chain, the tools and methods used.

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SAXS data reduction and analysis

Organiser: Michael Sztucki, contact
Monday 8 February: 14h00 - 16h00

Scope

Online data reduction and analysis are crucial for the productivity of any Small-Angle X-ray Scattering instrument especially when dealing with large amount of data or taking decision during a time-resolved experiment or radiation damage testing. The developed programs and tools do not only work at the ESRF beamline, but can also be installed at the home laboratory for more detailed data analysis.

This tutorial discusses the metadata concept and the (online) data reduction schemes implemented at the ID02 beamline: SPD (saxs programs) and PyFAI using the EDF or new HDF5 data format, respectively. It covers the understanding of the data formats, detector dependent corrections (non-linearity, dark current, flat field, spatial distortion, etc.) as well as the normalisation to an absolute intensity scale and the azimuthal integration to obtain one dimensional SAXS profiles. The second half of the tutorial is dedicated to the SAXSutilities program which allows data visualisation of multiple data sets, averaging, background subtraction, normalisation for sample thickness, error estimation, etc. In addition, routines for data masking, finding the beam centre, calibration of WAXS detector position, etc. are  implemented. More advanced features include direct modelling of the SAXS data in terms of standard models in small-angle scattering.

Short introduction to the available data reduction software at ID2

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Electronic Structure and Lattice dynamics calculations in complex systems

Organiser: Alexei Bosak (ESRF) and Björn WEHINGER (University of Geneva), contact
Monday 8 February: 14h00 - 17h30

Scope

This tutorial gives an introduction to electronic structure and lattice dynamics calculations based on density functional theory. Theoretical background and practical aspects are discussed in the first part. The following topics will be covered:

  • Exchange and correlation in DFT: approximations and applications to complex systems
  • Geometry optimization
  • Band structure
  • Phonons

The second part of the tutorial is dedicated to the calculation of scattering intensities for X-rays and neutrons:

  • Debye Waller factors
  • Dynamical structure factor
  • Thermal diffuse scattering
  • Inelastic scattering from phonons

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