Tutorials

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Remote data collection with EXI and MXCuBE3
D. De Sanctis & G. Santoni

This tutorial provides an introduction to the use of EXI (Extendend ISPyB) and MXCuBE3 to perform remote data collection at the ESRF Macromolecular Crystallography beamlines. The tutorial will be split in three parts:

1. Prepare experiment in EXI: showing how to upload samples and shipment information to EXI
2. Data collection with MXCuBE3: introducing the new interface of the data acquisition and the different data collection methods available in MXCuBE3
3. Data processing retrieval from EXI from different data collections

Getting the best out of MASSIF-1 and workflows at the ESRF
D. Nurizzo & M. Bowler

This tutorial will introduce the fully automated beamline MASSIF-1 and tips and tricks to get the best possible data from your samples. We will also cover the use of workflows on all the ESRF Macromolecular Crystallography beamlines.

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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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In this tutorial basic statistical concepts will be presented trying to present the amount of data as an advantage rather than an inconvenient.

The participants will learn about the capabilities offered by blind source separation techniques and basic clustering approaches.

Examples of application on microscopy experiments will be provided.

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Your research is finally ready to be published? Congratulations! But, let’s not forget that the research publication is not the end of the process, but the beginning of another one, also important: communication. Statistics show that global scientific output doubles every nine year. It means that mastering communication, and all communications tools, especially digital tools, is now crucial to promote your research. Press, social media, this tutorial aims to give you tips to optimise the promotion of your research.

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This tutorial proposes a reminder of the principles of the Laue Microdiffraction scattering technique and will showcase data analysis examples from data collected on the beamline. Digital image peak search, structure model refinement and batch analysis will be presented.

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Morning session

Introduction to pyFAI and hands-on to calibrate a SAXS and WAXS experiment together with data reduction for a diffraction mapping experiment.

Afternoon session

Advanced tutorial using Jupyter: calibration of a goniometer and associated data reductions.

Organisers	Kirill Lomachenko (ESRF) Yves Joly (ESRF) Francesco D'Acapito (ESRF)
Contact	contact
Date	Monday 8 February
Time	Common session: 9h00 - 12h00 / Introduction to XAS: The Whys, The Whats and The Hows Kirill Lomachenko Parallel sessions: 13h30 - 16h30 / Ab initio simulation of X-ray absorption spectroscopies using FDMNES    Yves Joly 13h30 - 16h30 / Introduction to the analysis if EXAFS data         Francesco D'Acapito
Equipment required / Instructions	Ab initio simulation of X-ray absorption spectroscopies using FDMNES: Participants must have a software for plotting (Origin, Kaleidagraph... NOT Excel). Introduction to the analysis if EXAFS data: Participants must use a proper computer with the the programs of the Athena & Artemis suite installed, and download the analysis codes at the address: http://bruceravel.github.io/demeter/
Format	Morning session: Zoom Webinar Afternoon session: Zoom Meeting

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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:

1. Learn the basic use of FDMNES
2. Make a series of numerical experiments to see the sensitivity of the spectroscopies to the material geometry and the beam polarization
3. 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 of 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.

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Coherent X-rays are a unique tool to access dynamics in condensed matter at the length scale probed by the scattering vector Q. This is achieved by quantifying the temporal correlation of the intensity fluctuations in a speckle patterns. Spontaneous and driven dynamics can be retrieved in the temporal domain down to 10^-6 s in a large variety of soft and hard matter 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.

The tutorial covers the fundamental principles of the coherence-based technique and details of the data collection. Special emphasis is put on the data analysis practice and interpretation of the results. Finally, we show how the hundred times increase in brilliance at the ESRF-EBS enables new exciting scientific prospects in the field.