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- User Meeting 2018
- Tutorials (Monday 5 February)
Tutorials (Monday 5 February)
12 tutorials for users will be organised on Monday 5 February.
Organisation of the tutorials:
Participants may sign up to only one tutorial and the number of participants for some tutorials is limited. You are expected to attend for the full duration of the tutorial you sign up for, so please select carefully the tutorial you wish to attend, register your participation via the registration form and do not forget to modify your registration form if you cannot attend to give the possibility to other scientists to register. Please note that, to ensure sufficient space for external participants, ESRF staff will not be able to register for tutorials until after the registration deadline (providing there are places left for the desired tutorial).
Organiser: Delphine Chenevier, ESRF, contact
Monday 5 February: 10h00 - 11h30
Scope
Science communication has now become part of a scientist's everyday life. Scientists have to give talks and write papers and proposals, but more and more often nowadays they also have to
communicate with a wide variety of media outlets to explain the issue and impact of their research. Scientists themselves are sometimes now embracing roles that were conventionally taken on by trained science communicators.
Navigating the busy science media ecosystem today can be daunting for you as researchers. There are broadcast, print and online media outlets to talk to, a wide variety of social networks to use as platforms for networking and sharing your research, as well as digital media products that promise to translate your work for broader audiences.
You may have a hard time deciding what platforms are best for communicating your work, and how to adapt to the diversity of audiences and provide the best materials to these different media channels. In the tutorial we will discuss these issues as well as addressing how we can efficiently use these tools that are in constant evolution, and how the ESRF is dealing with these different media channels for communicating Science.
Organisers: Gordon Leonard, Deborah Davison, ESRF, contact
Monday 6 February: 8h30 - 18h30
Scope
A meeting of ESRF BAG Responsibles (by invitation only) that includes presentation of current and future ESRF facilities for Structural Biology - including cryo-EM, visits to current end-stations and a round table discussion concerning the future of Structural Biology Facilities at ESRF.
Organiser: Armando Sole, ESRF, contact
Monday 5 February: 14h00 - 18h00
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.
Organiser: Sakura Pascarelli, ESRF, contact
Morning session (9h00 - 12h30): Introduction to XAS and EXAFS (all participants)
Afternoon session (14h00 - 18h00): Parallel sessions
Scope
Introduction to XAS and EXAFS
This tutorial provides a very general introduction to the fundamentals of X-ray absorption spectroscopy. The origin 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 distances, coordination 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 breakthroughs to a selection of recent results at the ESRF.
Parallel sessions
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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.
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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 .
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EXAFS practical on beamlines BM25 and BM08 (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.
Organiser: Federico Zontone, Beatrice Ruta, Yuriy Chshkin, ESRF, contact
Monday 5 February: 9h00 - 12h00
Scope
X-ray photon correlation spectroscopy (XPCS) is a unique scattering technique which exploits the coherent fraction of the beam to probe slow (currently 10-4-104 s) spontaneous and driven collective dynamics in materials. XPCS is routinely used to measure spatio-temporal fluctuations in a variety of soft and hard-condensed matter systems, e.g. colloids, gels, phase-ordering alloys, glasses covering nanometric and even atomic length scales. XPCS is the only technique able to probe the slow (10-104 s) equilibrium and non-equilibrium relaxation processes in deeply super-cooled melts and structural glasses.
This tutorial provides the fundamental principles of the technique and details of the data collection. Special emphasis is put on the data analysis practice and interpretation of the results. The tutorial will end with a discussion on the future XPCS beamline that will be built in view of the 100 times increase in brilliance at the ERSF-EBS.
Programme
9:00-9:50 XPCS foundations and experiments - Federico Zontone
9:50-10:00 Break
10:00-11:00 XPCS data analysis tools and practice - Yuriy Chushkin
11:00-11:10 Break
11:10-12:00 XPCS future perspectives with EBS - Beatrice Ruta
Organiser: Alexander Rack, ESRF, contact
Monday 5 February: 10h00 - 18h30
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. Dedicated time will be reserved to discuss with experts on an individual basis.
Participants are welcome to bring their own data sets for preliminary tests and discussion.
Organiser: Michael Sztucki, ESRF, contact
Monday 5 February: 14h00 - 16h00
Scope
The seminar covers in a first part an introduction to good practice of (U)SAXS/WAXS data recording for quantitative analysis. The necessary SAXS theory and its appropriate experimental implementation will be discussed as well as (on-line) data reduction steps and data formats.
The second more practical part of the presentation is dedicated to analysis strategies of SAXS data. This covers simple approaches like Porod and Guinier analysis, an introduction to form and structure factors and model fitting. Typical examples from the field of soft matter illustrate the presentation, using software available for on-line data reduction and visualisation at beamline ID02 (SAXSutilities, saxs programs, spd, PyFAI). An overview and practical demonstration of other available fitting programs like sasview, sasfit, Irena will completes the tutorial.
Organiser: Dimitrios Bessas, Aleksandr Chumakov, Rudolf Rüffer, ESRF, contact
Monday 5 February: 9h00 - 18h00
Scope
This hands-on tutorial will
- give an introduction to the capabilities of the Nuclear Resonance beamline (ID18) with special emphasis to Mössbauer spectroscopy with the synchrotron Mössbauer source (SMS),
- give an introduction to data evaluation software and
- allow for following an experiment at the beamline. For the latter topic participants are encouraged to bring their own sample(s) for a test measurement in transmission geometry (57Fe, focused beam size about 15 mircometer in diameter).
- Eventually, you should be able to evaluate the taken Mössbauer spectra from your successful measurement.
Organiser: Marius Retegan, ESRF, contact
Monday 5 February: 9h00 - 12h00
Scope
The goal of the tutorial is to familiarize the participants with the simulation of core-level spectra using semi-empirical multiplet approaches. Following a short introduction of the theoretical aspects, a hands-on training will be given. This will include examples of simulating X-ray absorption (XAS) and resonant inelastic X-ray scattering (RIXS) spectra for transition metals and rare earths.
All simulations will be performed using Crispy (http://www.esrf.eu/computing/scientific/crispy), a modern user interface for the Quanty software package (http://www.quanty.org).
The participants are asked to bring their laptops.
Organiser: Jean-Sébastien Micha, ESRF, contact
Monday 5 February: 9h00- 12h00
Scope
Polychromatic (Laue) diffraction at submicrometer scale: main steps of analysis of simple and single to complex and numerous Laue patterns. The tutorial will cover the main concepts and algorithms involved in the standard analysis which are implemented in modules of the software suite LaueTools including Graphical User Interfaces and scripting capabilities: digital image processing, laue pattern indexation, orientation & strain refinement and 2D peak shape simulation. Examples will be given using data images recorded at the ESRF on CRG-IF BM32 beamline. Typical notebooks for sample 2D map data analyses will also be handled.
LaueTools can be installed on laptops before the tutorial at http://sourceforge.net/projects/lauetools/
Organiser: Diego Pontoni, ESRF, contact
Monday 5 February:
9h00-12h00: Oral presentations
14h00-17h30: Practicals (2 groups of 4 doing all 3 practicals)
Scope
The ESRF and ILL users proposals contain an increasing number of projects requiring the use of multiple synchrotron and neutron methods in combination with several lab-based complementary characterization techniques. This trend is particularly evident in the field of soft matter, where the success of the scheduled beamtime often critically depends on the availability of suitable lab space and tools for the on-site preparation, manipulation and assessment of fresh metastable samples. In order to simultaneously offer their users cutting-edge state-of-the-art beamlines and advanced complementary support, the ESRF and ILL have established the Partnership for Soft Condensed Matter (PSCM). The PSCM is located in a shared building (Science Building) which is physically connected to both the ESRF and ILL experimental halls and it hosts a dozen of support laboratories dedicated to e.g. light scattering, ellipsometry, optical spectroscopy and calorimetry. All tools and services - ranging from ovens, centrifuges and Langmuir troughs to the design and production of personalized 3D-printed sample environments - are offered to all onsite researchers regardless of their status of ESRF/ILL user/staff. As a result, the PSCM labs are exploited by a core majority of soft matter scientists plus an increasing number of researchers active in e.g. chemistry, biology, life and materials sciences and even in some cases hard condensed matter.
The morning will be dedicated to oral presentations detailing the PSCM concept and the offered techniques, instruments and services. The afternoon will feature a series of three practical sessions focusing on (1) atomic force microscopy, (2) microfluidics and 3D printing, and (3) optical microscopy. During the closing discussion the participants will have an opportunity to express their wishes regarding further improvement of the services offered by the PSCM.
Organiser: Vincent Favre Nicolin, ESRF, contact
Monday 5 February: 14h00- 18h00
Scope
Presentation and application of PyNX (http://ftp.esrf.eu/pub/scisoft/PyNX/).
The tutorial will cover algorithms and examples using Coherent Diffraction Imaging (2D and 3D), Ptychography, wavefront propagation. (+To be confirmed: phase contrast imaging). Different algorithmes will be presented (difference map, alternating projections, HIO, Error Reduction etc..)
Examples will be given using 2D (and 3D for CDI) datasets. The participants will be able to use both scripts for automated analysis (no programming knowledge required), and example python code for advanced use.
Pre-requisite to run the hands-on practical: knowledge in running command-line scripts for analysis. Basic python knowledge to test the python API. Calculations will be performed remotely on GPU machines, accessed via wi-fi from laptops or the ESRF training room desktop.
partners
European Synchrotron Radiation Facility - 71, avenue des Martyrs, CS 40220, 38043 Grenoble Cedex 9, France.