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- User Meeting 2020
- Tutorials (Monday 3 February)
Tutorials (Monday 3 February)
Organisation of the tutorials
Participants may sign up to only one tutorial and some tutorials can only have a limited amount of participants. You are expected to attend for the full duration of the tutorial you sign up for, so please carefully select the tutorial you wish to attend.
You must register to the desired tutorial via the Registration Form. If you cannot attend your tutorial, please modifiy your registration so that other scientists may register.
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 can register on a waiting list of the desired tutorial through their electronic registration form (see page "Questions").
List of tutorials
Organisers | Serial crystallography data processing: G. Santoni (ESRF) M. Nanao (ESRF) BAG Meeting: Gordon Leonard (ESRF) David Flot (ESRF) Deborah Davison (ESRF) |
Contact | contact |
Date | Monday 3 February |
Time & Venue | 9h - 12h / Room to be confirmed : Merging of Serial crystallographic data by Hierarchical Cluster Analysis and Genetic Algorithms 14h - 17h30 / CIBB Seminar room: BAG Meeting (by invitation only) |
SCOPE
This tutorial is divided into two parts:
- Merging of Serial crystallographic data by Hierarchical Cluster Analysis and Genetic Algorithms
- BAG Meeting (by invitation only)
Merging of Serial crystallographic data by Hierarchical Cluster Analysis and Genetic Algorithms
Morning
Fixed target serial experiments are now available on all MX beamlines at the ESRF, via the Mesh and Collect workflow. This form of serial crystallography has the advantage of requiring no complicated sample preparation measures. Indeed, sample preparation is typically as simple as scooping up a slurry of crystals in a mesh or large loop and then flash freezing. In this tutorial, we will demonstrate how to use two in house software packages to select which of the large number of partial datasets should be merged together.
BAG meeting
Afternoon
This meeting is by invitation only.
General scope : impact of EBS on SB beam lines.
Organisers | Kirill Lomachenko (ESRF) Yves Joly (CNRS) Francesco D'Acapito (LISA/BM08) |
Contact | contact |
Date | Monday 3 February |
Time & Venue | Common session: 9h - 12h / ILL Chadwick Amphitheater: Introduction to XAS: The Whys, The Whats and The Hows Kirill Lomachenko Parallel sessions: 14h - 17h / Room BEL-1-01: Ab initio simulation of X-ray absorption spectroscopies using FDMNES Yves Joly 14h - 17h / Room 337: Introduction to the analysis of EXAFS data Francesco D'Acapito |
Equipment required / Instructions | Ab initio simulation of X-ray absorption spectroscopies using FDMNES: Participants must bring their own laptop (Mac, Windows or Linux) and have a software to plot spectra (Origin, Keleidagraph... NOT Excel). Introduction to the analysis of EXAFS data: Participants must bring their own laptops and load the (free) software on their machines before coming. |
SCOPE
This tutorial provides a general introduction to X-ray absorption spectroscopy (XAS) techniques (mainly XANES and EXAFS). It consists of three different parts.
In the morning session general introductory lecture will be given, highlighting the physical bases of the XAS methods, types of structural and electronic information that can be extracted from XAS data, variety of XAS data analysis approaches, peculiarities of XAS experimental setups, as well as the recent case-studies carried out in ESRF.
In the afternoon, two parallel sessions will be organised, focusing on ab initio XAS simulations and EXAFS data analysis, respectively. Details of the parallel sections are given below.
Ab initio simulation of X-ray absorption spectroscopies using FDMNES
Yves Joly
After a short introduction on XANES, X-ray Raman, and valence to core X-ray Emission spectroscopy, and the specificities of FDMNES, most of the tutorial will be devoted to:
- Learn the basic use of fdmnes
- Make a series of numerical experiments to see the sensitivity of the spectroscopies to the material geometry and the beam polarization
- Start case study proposed by the participants
Introduction to the analysis of EXAFS data
Francesco D'Acapito
This introduction to the XAS technique will consist a tutorial on the basic data analysis. After a first example students will be invited to carry out themselves the analysis on a variety of cases.
Organisers | Yuriy Chushkin (ESRF) Beatrice Ruta (UCB Lyon 1, CNRS UMR 5306) Federico Zontone (ESRF) |
Contact | contact |
Date | Monday 3 February |
Time & Venue | 9h - 10h / EMBL Seminar room: Introduction to coherent X-ray scattering Common introduction with Tutorial T4. 10h15 - 12h15 / EMBL Seminar room:
|
SCOPE
Coherent X-rays are a unique probe to access the microscopic arrangement occurring in a material depending on the Q-vector of the scattering experiment. In X-ray Photon Correlation Spectroscopy (XPCS) one measures X-ray speckles fluctuations in time that allow probing spontaneous and driven collective dynamics in the temporal domain (currently 10-5-104 s). XPCS can be applied to a large variety of soft and hard matter systems, to measure dynamics 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.
The tutorial covers 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. Finally, we discuss how the hundred times increase in brilliance at the ERSF-EBS enables new exciting scientific prospects in the field.
Organisers | Vincent Favre Nicolin (ESRF) Steven Leake (ESRF) Manfred Burghammer (ESRF) Peter Cloetens (ESRF) |
Contact | contact |
Date | Monday 3 February |
Time & Venue | 9h - 10h / EMBL Seminar room: Introduction to coherent X-ray scattering Common introduction with Tutorial T3. 10h15 - 12h30 / Room LOB-1-45: Lecture: introduction to coherent imaging techniques 14h - 17h / Room LOB-1-45: Hands-on data analysis using PyNX |
Equipment required / Instructions | Hands-on data analysis using PyNX: Participants will need their own laptops for data analysis |
SCOPE
This tutorial will start in the morning with a series of lectures introducing coherent X-ray imaging techniques: phase contrast imaging, coherent diffraction imaging and ptychography in the small-angle and Bragg geometry. In the afternoon a hands-on tutorial (laptop required) will be given on data analysis for coherent diffracion imaging and ptychography, using the PyNX software package . This tutorial is suitable for all (beginners or experienced scientists).
Organisers | Alexander Rack (ESRF) |
Contact | contact |
Date | Monday 3 February |
Time & Venue | 10h - 12h & 13h30 - 15h / Room MD-1-21: Lecture session 15h30 - 18h30 / Room MD-1-21: Practical, questions & demonstrations |
Equipment required / Instructions | Participants can bring their own data sets on USB key for preliminary tests and discussion. |
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.
Organisers | Michael Sztucki (ESRF) |
Contact | contact |
Date | Monday 3 February |
Time & Venue | 14h - 16h / EMBL Seminar room |
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.
Organisers | Jean-Sébastien Micha (CEA Grenoble - INAC) |
Contact | contact |
Date | Monday 3 February |
Time & Venue | 9h - 12h30 / Room 03-1-13 |
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/
Organisers | Jerome Kieffer (ESRF) |
Contact | contact |
Date | Monday 3 February |
Time & Venue | 9h - 12h / Room 500-501 |
Equipment required | Participants will need their own laptops with working WIFI. |
SCOPE
This tutorial presents the data reduction pipeline for preparing scattering data acquired with 2D detectors using the pyFAI software suite, focusing on the usage of the different graphical user interfaces.
- Calibration of the experimental setup: detector position
- Dark current, flat-field correction and data averaging with HDF5 data files
- Azimuthal integration: single frame and batch processing
- Diffraction imaging.
The participants are asked to bring their laptops to be able to practice. The software is available as part of the silx project at: https://github.com/silx-kit/pyFAI
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