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- User Meeting 2019
- Tutorials (Monday 4 February)
Tutorials (Monday 4 February)
9 tutorials for users will be organised on Monday 4 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.
One exception however, the tutorial T9: round-table discussion on "Gender parity in science" which will take place during lunch is open to all. So you can register even if you are already registered for another tutorial. The number of participants is limited to 50.
Registration of ESRF Staff for a tutorial
To ensure sufficient space for external participants, ESRF staff will not be able to register for tutorials until after the registration deadline, and providing there are places left for the desired tutorial.
ESRF staff interested in participating in a tutorial have the possibility to register on a waiting list of the desired tutorial through their electronic registration form (see page "Questions").
Organisers:
Marine Cotte (ESRF)
Hiram Castillo-Michel (ESRF)
Alejandro Fernandez Martinez (ISTerre, Grenoble)
Administrative support: Sonya Girodon, Eva Jahn, Claudine Roméro (ESRF)
contact
Venue: IBS Seminar room
Date: Monday 4 February - 8h50-18h30
Scope
Biological systems are by essence fragile materials. Their studies by synchrotron radiation techniques require a careful consideration of their preservation: this includes a cautious preparation that preserves the native structures, but also an adapted sample environment and data collection mode that preserve the samples during data acquisition and reduce the beam damages, to ensure the reliability of the results and preserve the samples for possible future measurements. These issues will be all the more so important with EBS.
The multi-scale capabilities of the SR techniques allow studying biological systems from proteins and cells up to tissues or even organs level. Techniques are different but all share challenges in terms of sample preparation and preservation. This discussion proposes to expert and non-expert users from various communities to meet and exchange ideas about protocols developed both for assessing and understanding radiation damage but also for preparing and preserving biological samples for X-ray analyses.
The tutorial will be based on presentations from the following experts:
- Dr. Martin Weik (Institut de Biologie Structurale, Grenoble, France)
General introduction about radiation damage on protein crystals - Dr. Antoine Royant (Institut de Biologie Structurale, Grenoble, France)
- Dr. Pieter Glatzel (ESRF, Grenoble, France)
Radiation damage observed in XAS analyses - Dr. Paul Tafforeau (ESRF, Grenoble, France)
Assessing the impact of X-ray tomography on fossils DNA - Dr. Hélène Malet (Institut de Biologie Structurale, Grenoble, France)
Preparing biological samples for cryo EM - Dr Sylvain Bohic (Grenoble Institut Neurosciences, Grenoble, France)
Preparation and observation (cryo visible microscope) of samples for nano-scopy at ID16A - Dr. Katarina Vogel-Mikus (Univerza v Ljubljani, Slovenia, France)
Preparation of tissues for μXRF/μXAS analyses - Dr. Giulia Veronesi (CNRS, Grenoble)
Optimizing cells preparation for correlative elemental imaging/electron microscopy - Dr. Karim Benzerara (Sorbonne University, Paris)
Cryo-ultramicrotomy (CEMOVIS), STXM, cryo-STXM and cryo-SEM study of mineral formation by bacteria
Information about ESRF access and on-site services will also be presented by:
- Dr. Véronique Mayeux (ESRF)
Safety rules for the analysis of biological samples at the ESRF and overview of the labs on site - Peter Van der Linden (ESRF)
The cryo stage for ID13/ID16B - Pierre Lloria (ESRF)
The PSCM: Instruments available for off line pre/post characterization
If you wish to contribute to the discussion by presenting your own developments, please contact the organizers
Organiser:
Sakura Pascarelli, ESRF, contact
Date: Monday 4 February
- Morning session (9h00-12h30): Introduction to XAS and EXAFS (all participants)
Venue: ILL Chadwick Amphitheatre
- Afternoon session (14h00-18h00): Parallel sessions
Venues: see below
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)
Venue: meeting room 03 1-13
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)
Venue: meeting room 03 1-07
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, Linux or MAC) with a software to plot spectra (Origin, Kaleidagraph...)
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Visit of FAME and FAME-UHD (maximum of 8 participants) - CANCELLED
Following the general introduction to XAS and EXAFS done in the morning, this visit of both FAME (French Absorption spectroscopy beamline in Material and Environmental sciences) and FAME-UHD (Ultra High Dilution) beamlines will be a perfect opportunity to discover the specificities of a XAS beamline, and the requirements of XAS measurements. The potential of XAS, especially for challenging samples, will be detailed with the presentation of real world examples. With the visit of FAME-UHD we'll introduce the improvements provided by high energy resolution detection set-ups (crystal analyzers) and the opportunities they offer to XAS users.
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Introduction to the XAS technique (maximum of 4 participants)
Beamline Simulator BM08
This introduction to the XAS technique will consist in a first part focused on data collection (how to prepare a sample, how to choose a proper data collection strategy, ...) and will make use of the beamline simulator. In the second part the data analysis (in a simple version, just the first shell) will be presented and if time is available students will have the opportunity of carrying it out themselves on the data just 'collected'.
ESRF organisers:
Federico Zontone, Yuriy Chushkin, Julio Cesar da Silva, contact
UOC organisers:
Oier Bikondoa, Beatrice Ruta
Venue: EMBL seminar room 9-10
Date: Monday 4 February - 9h00-12h00
Scope
Modern X-ray sources provide intense beams with high degree of coherence and unique capabilities to probe the microscopic arrangements occurring in a material. Under coherent illumination, the X-ray scattering pattern shows a grainy intensity distribution called speckle pattern. Such speckle pattern depends on the exact instantaneous structure of the sample. X-ray Photon Correlation Spectroscopy (XPCS) analyses the temporal speckle intensity fluctuations and can provide information about spontaneous and driven collective dynamics in the 10-5-104 s time range, in a large variety of soft and hard systems, e.g. from the meso-scale in colloids, gels and phase-ordering alloys, down to the atomic length scale in deeply super-cooled melts and structural glasses.
An oversampled static speckle pattern can be inverted to obtain a high resolution image of the scattering object using phase retrieval methods. The two typical techniques are Coherent Diffraction X-ray Imaging (CXDI) and ptychography, whose applications depend on the size and characteristics of the sample. When combined with tomography, CXDI and ptychography can provide quantitative high resolution 3D images of objects with sizes ranging from micrometers to millimetres. The spatial resolution is limited by the highest scattering vector where speckles are recorded rather than by the size of the beam or the pixel size of the detector.
The tutorial aims to provide basic knowledge of the coherent properties of X-ray sources and to illustrate applications of coherent X-rays for imaging and dynamics studies. Finally, we will outline the exciting perspectives with the ERSF-EBS, where coherence areas and intensities of are promised to increase up to 100 times.
Programme
9:00-9:40 Modern X-ray sources and coherence - Federico Zontone
9:45-9:55 Break
9:55-10:35 XPCS: Principles and highlights - Yuriy Chushkin
10:40-10:50 Break
10:50-11:30 Ptychographic CXDI: Principles and highlights – Julio Cesar da Silva
11:35-12:00 Future perspectives with EBS - Beatrice Ruta & O. Bikondoa
Organiser:
Alexander Rack, ESRF, contact
Venue: Meeting room MD-1-21
Date: Monday 4 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
Venue: EMBL Seminar room 9-10
Date: Monday 4 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:
Marius Retegan, ESRF, contact
Venue: meeting room BEL 1-01
Date: Monday 4 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
Venue: meeting room MF-1-06 MTBF
Date: Monday 4 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:
Vincent Favre Nicolin, ESRF, contact
Venue: meeting room MF-1-06 MTBF
Date: Monday 4 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.
Organisers:
Michela Brunelli and Beatrice Ruta (ESRF User Organisation) in collaboration with the ESRF Communication Unit, contact
Venue: ESRF Auditorium
Date: Monday 4 February - 12h00–14h00
Scope
Roundtable on Gender parity in science. Debated questions will include "Do women and men have equal opportunities in scientific research and academia? How traditional gender roles hold back female scientists? How long until women and men are equally represented in science?"
It will take place at the ESRF during the first day of the ESRF User Meeting, and will be animated by Giovanna Fragneto (Large Scale Structures Group Leader, ILL) and Nedjma Bendiab (lecturer at Université Grenoble Alpes and scientist at Institut NEEL).
The Roundtable will be followed by a buffet lunch offered to all participants.
Invited Speakers are:
- Cornelius Gross, Deputy Head, EMBL-Rome
- Eva Pebay-Peyroula, former IBS Director
Invited Guests are:
- Christiane Alba-Simionesco, CEA, former LLB Director
- Brigitte Plateau, General Administrator of Grenoble-INP and "Directrice Générale de l'enseignement supérieur et de l'insertion professionnelle en Conseil des Ministres"
- Jean Daillant, Soleil Synchrotron General Director
- Sine Larsen, former ESRF Director
Download the programme and the flyer.
partners
European Synchrotron Radiation Facility - 71, avenue des Martyrs, CS 40220, 38043 Grenoble Cedex 9, France.