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Darfix: DFXM Data Analysis Tool

This video introduces Darfix, a Python-based data anlaysis package for dark-field X-ray microscopy

Scientific topics: x-ray microscopy

Keywords: Darfix, DFXM, Dark-field X-ray microscopy

Resource type: video

Darfix: DFXM Data Analysis Tool https://pan-training.eu/materials/darfix-dfxm-data-analysis-tool This video introduces Darfix, a Python-based data anlaysis package for dark-field X-ray microscopy x-ray microscopy Darfix, DFXM, Dark-field X-ray microscopy
"Processing tomographic data with tomwer software Step 4 - Reconstruct volume"

This video shows how tprocess tomographic data with tomwer (4/4), focusing on reconstructing volume

Scientific topics: tomography

Resource type: video

"Processing tomographic data with tomwer software Step 4 - Reconstruct volume" https://pan-training.eu/materials/processing-tomographic-data-with-tomwer-software-step-4-reconstruct-volume This video shows how tprocess tomographic data with tomwer (4/4), focusing on reconstructing volume tomography
"Processing tomographic data with tomwer software Step 3 - Run the workflow automated edf"

This video shows how tprocess tomographic data with tomwer (3/4), focusing on running workflow automated edf

Scientific topics: tomography

Keywords: tomography, tomwer

Resource type: video

"Processing tomographic data with tomwer software Step 3 - Run the workflow automated edf" https://pan-training.eu/materials/processing-tomographic-data-with-tomwer-software-step-3-run-the-workflow-automated-edf This video shows how tprocess tomographic data with tomwer (3/4), focusing on running workflow automated edf tomography tomography, tomwer
Processing tomographic data with tomwer software Step 2 - Run the workflow interaction hdf5

This video shows how tprocess tomographic data with tomwer (2/4), focusing on running a workflow interaction hdf5

Scientific topics: tomography

Keywords: tomography, tomwer

Resource type: video

Processing tomographic data with tomwer software Step 2 - Run the workflow interaction hdf5 https://pan-training.eu/materials/processing-tomographic-data-with-tomwer-software-step-2-run-the-workflow-interaction-hdf5 This video shows how tprocess tomographic data with tomwer (2/4), focusing on running a workflow interaction hdf5 tomography tomography, tomwer
Processing tomographic data with tomwer software Step 1 - Create the workflow

This video shows how tprocess tomographic data with tomwer (1/4), focusing on creating the workflow

Scientific topics: tomography

Keywords: tomography, tomwer

Resource type: video

Processing tomographic data with tomwer software Step 1 - Create the workflow https://pan-training.eu/materials/processing-tomographic-data-with-tomwer-software-step-1-create-the-workflow This video shows how tprocess tomographic data with tomwer (1/4), focusing on creating the workflow tomography tomography, tomwer
Powder X-ray diffraction phase identification with QualX2*

This video shows how to identify powder X-Ray difraction phases with QualX2*

Scientific topics: powder diffraction

Keywords: Powder Diffraction, QualX2*

Resource type: video

Powder X-ray diffraction phase identification with QualX2* https://pan-training.eu/materials/powder-x-ray-diffraction-phase-identification-with-qualx2 This video shows how to identify powder X-Ray difraction phases with QualX2* powder diffraction Powder Diffraction, QualX2*
X-ray diffraction image calibration using PyFAI and Jupyter notebook

"This video shows how to calibrate an X-Ray Diffraction Image using PyFAI and Jupyter Notebook "

Scientific topics: x-ray diffraction

Keywords: X-ray Diffraction, pyFAI, jupyter notebook

Resource type: video

X-ray diffraction image calibration using PyFAI and Jupyter notebook https://pan-training.eu/materials/x-ray-diffraction-image-calibration-using-pyfai-and-jupyter-notebook "This video shows how to calibrate an X-Ray Diffraction Image using PyFAI and Jupyter Notebook " x-ray diffraction X-ray Diffraction, pyFAI, jupyter notebook
Displaying ID21 XANES Spectra with PyMca

This video shows how to display X-Ray Absorption Near Edge Structure (XANES) spectra from ID21 beamline at the ESRF with PyMca

Scientific topics: x-ray absorption near edge structure

Keywords: PyMca, xanes

Resource type: video

Displaying ID21 XANES Spectra with PyMca https://pan-training.eu/materials/displaying-id21-xanes-spectra-with-pymca This video shows how to display X-Ray Absorption Near Edge Structure (XANES) spectra from ID21 beamline at the ESRF with PyMca x-ray absorption near edge structure PyMca, xanes
Visualising fitted ID21 XRF maps with PyMca

This video shows how to visualise fitted X-Ray Flourescence (XRF) maps from ID21 beamline at the ESRF with PyMca

Scientific topics: x-ray fluorescence

Keywords: PyMca, X-ray fluorescence

Resource type: video

Visualising fitted ID21 XRF maps with PyMca https://pan-training.eu/materials/visualising-fitted-id21-xrf-maps-with-pymca This video shows how to visualise fitted X-Ray Flourescence (XRF) maps from ID21 beamline at the ESRF with PyMca x-ray fluorescence PyMca, X-ray fluorescence
Integrator documentation

Documentation for Integrator, a distributed azimuthal integration software used at the European Synchrotron Radiation Facility (ESRF)

Scientific topics: scattering technique, powder diffraction

Keywords: computation distribution, azimuthal integration, high-performance

Resource type: Document

Integrator documentation https://pan-training.eu/materials/integrator-documentation Documentation for Integrator, a distributed azimuthal integration software used at the European Synchrotron Radiation Facility (ESRF) scattering technique powder diffraction computation distribution, azimuthal integration, high-performance
Tomo-tools training

Training modules available for the different tomography tools at the European Synchrotron Radiation Facility (ESRF)

Scientific topics: tomography

Keywords: tomography

Resource type: Document

Tomo-tools training https://pan-training.eu/materials/tomo-tools-training Training modules available for the different tomography tools at the European Synchrotron Radiation Facility (ESRF) tomography tomography
Nabu documentation

Documentation for Nabu, a tomography software used at the European Synchrotron Radiation Facility (ESRF)

Scientific topics: tomography

Keywords: tomography, reconstruction, full-field, phase contrast, high-performance

Resource type: Document

Nabu documentation https://pan-training.eu/materials/nabu-documentation Documentation for Nabu, a tomography software used at the European Synchrotron Radiation Facility (ESRF) tomography tomography, reconstruction, full-field, phase contrast, high-performance
Make Your Research Reproducible

Making your work reproducible may seem daunting right now, but we’ll take it step by step and you can choose what you want to implement now and what you want to keep for later. This is a process and there is no need to take all the steps at once. Let’s just try to move towards reproducible on the...

Keywords: reproducibility, version control, project management, FAIR

Make Your Research Reproducible https://pan-training.eu/materials/make-your-research-reproducible Making your work reproducible may seem daunting right now, but we’ll take it step by step and you can choose what you want to implement now and what you want to keep for later. This is a process and there is no need to take all the steps at once. Let’s just try to move towards reproducible on the reproducibility scale. reproducibility, version control, project management, FAIR
Computational Reproducibility with the shell, Git and Docker

This workshop provides an overview over tools for computational reproducibility in research. At the end of this workshop participants will be able to navigate via the shell and use it for version control with Git. They will know what types of projects require which forms of computing environments...

Keywords: scientific software, reproducibility, docker container, version control, shell

Resource type: slides

Computational Reproducibility with the shell, Git and Docker https://pan-training.eu/materials/computational-reproducibility-with-the-shell-git-and-docker This workshop provides an overview over tools for computational reproducibility in research. At the end of this workshop participants will be able to navigate via the shell and use it for version control with Git. They will know what types of projects require which forms of computing environments and be able to set up a Docker container to run computations in a reproducible way. scientific software, reproducibility, docker container, version control, shell research data scientist PhD students researchers scientists
Video introduction to data management plans for PaN users

Video guide illustrating the essential steps of creating a data management plan for an experiment.

Keywords: data management, DMP

Resource type: video

Video introduction to data management plans for PaN users https://pan-training.eu/materials/video-introduction-to-data-management-plans-for-pan-users Video guide illustrating the essential steps of creating a data management plan for an experiment. data management, DMP PaN users researchers
KFN Neutron Webinar

Lectures of the KFN Neutron Webinar, which are held monthly since April 2023. We thank all the speakers who have agreed to have their presentation shared in this collection, curated by Thomas Gutberlet and Karin Griewatsch.

Keywords: neutron, spallation, European Spallation Source, energy technology, COVID, inhibitors, quantum topology, neutrinos, High Brilliance Neutron Source, HBS, HiCANS, neutron source, ISIS,

Resource type: video

KFN Neutron Webinar https://pan-training.eu/materials/kfn-neutron-webinar Lectures of the KFN Neutron Webinar, which are held monthly since April 2023. We thank all the speakers who have agreed to have their presentation shared in this collection, curated by Thomas Gutberlet and Karin Griewatsch. neutron, spallation, European Spallation Source, energy technology, COVID, inhibitors, quantum topology, neutrinos, High Brilliance Neutron Source, HBS, HiCANS, neutron source, ISIS, scientists students
Tutorials for Nexus - Nuclear Elastic X-ray scattering Universal Software

Tutorials for the software package Nexus. The Nuclear Elastic X-ray scattering Universal Software (Nexus) is a Python package for simulating and fitting of Moessbauer spectra, nuclear resonant scattering (NRS) data, pure electronic X-ray reflectivities (XRR), nuclear X-ray reflectivities (nXRR),...

Scientific topics: nuclear resonant scattering, resonant scattering

Tutorials for Nexus - Nuclear Elastic X-ray scattering Universal Software https://pan-training.eu/materials/tutorials-for-nexus-nuclear-elastic-x-ray-scattering-universal-software Tutorials for the software package Nexus. The Nuclear Elastic X-ray scattering Universal Software (Nexus) is a Python package for simulating and fitting of Moessbauer spectra, nuclear resonant scattering (NRS) data, pure electronic X-ray reflectivities (XRR), nuclear X-ray reflectivities (nXRR), and polarization dependent electronic scattering. nuclear resonant scattering resonant scattering
Nexus - Nuclear Elastic X-ray scattering Universal Software

Repositroy for the Nexus. The Nuclear Elastic X-ray scattering Universal Software (Nexus) is a Python package for simulating and fitting of Moessbauer spectra, nuclear resonant scattering (NRS) data, pure electronic X-ray reflectivities (XRR), nuclear X-ray reflectivities (nXRR), and polarization...

Scientific topics: nuclear resonant scattering, reflectometry, polarimetry

Keywords: Nuclear Physics, Mossbauer spectroscopy, Nuclear resonant scattering

Resource type: software

Nexus - Nuclear Elastic X-ray scattering Universal Software https://pan-training.eu/materials/nexus-nuclear-elastic-x-ray-scattering-universal-software Repositroy for the Nexus. The Nuclear Elastic X-ray scattering Universal Software (Nexus) is a Python package for simulating and fitting of Moessbauer spectra, nuclear resonant scattering (NRS) data, pure electronic X-ray reflectivities (XRR), nuclear X-ray reflectivities (nXRR), and polarization dependent electronic scattering. nuclear resonant scattering reflectometry polarimetry Nuclear Physics, Mossbauer spectroscopy, Nuclear resonant scattering researchers scientists
X-ray reflectivity python scripts

The reflec_xraydb.py script generates reflectivity data files for materials using the XrayDB library. The plot_coatings_m2ab.py launches an animation plotting reflectivities as a function of energy for different angles for Palladium, Platinum and Boron carbide. The plot_coatings_m1.py...

Keywords: X-ray, reflectivity

X-ray reflectivity python scripts https://pan-training.eu/zenodomaterials/x-ray-reflectivity-python-scripts The reflec_xraydb.py script generates reflectivity data files for materials using the XrayDB library. The plot_coatings_m2ab.py launches an animation plotting reflectivities as a function of energy for different angles for Palladium, Platinum and Boron carbide. The plot_coatings_m1.py launches an animation plotting reflectivities as a function of energy for different angles for Iridium. X-ray, reflectivity
Training and learning platform Workshop: "EOSC, un atout pour la recherche"

Presentation that was done at the workshop: "EOSC, un atout pour la recherche" about the training platform.

Keywords: expands, PaNOSC, EOSC

Training and learning platform Workshop: "EOSC, un atout pour la recherche" https://pan-training.eu/zenodomaterials/training-and-learning-platform-workshop-eosc-un-atout-pour-la-recherche Presentation that was done at the workshop: "EOSC, un atout pour la recherche" about the training platform. expands, PaNOSC, EOSC
ExPaNDS Workshop - Follow a user story! A journey through the PaN data services.

The ExPaNDS Workshop "Follow a user story", which took place on the 24th of January in Hamburg, Germany (hybrid), aimed to provide a "User Journey", taking the audience on the road of the "European Open Science Cloud Photon and Neutron Data Services". The objective was to demonstrate how as...

Keywords: expands, EOSC, data services, FAIR, VISA, PaN portal

Resource type: slides, video

ExPaNDS Workshop - Follow a user story! A journey through the PaN data services. https://pan-training.eu/zenodomaterials/expands-workshop-follow-a-user-story-a-journey-through-the-pan-data-services The ExPaNDS Workshop "Follow a user story", which took place on the 24th of January in Hamburg, Germany (hybrid), aimed to provide a "User Journey", taking the audience on the road of the "European Open Science Cloud Photon and Neutron Data Services". The objective was to demonstrate how as a user, one can benefit from the services developed during the project. The story began with a FAIR journey presented by Brian Matthews, an EOSC demo from Marta Gutierrez, followed by a demo of the training platform from Oliver Knodel. The last two stops of the journey were two demos from the VISA portal (Silvan Schoen and Michael Schuh) and the search API/Harvesting services (PaN Portal, etc) presented by Carlo Minotti. The session was chaired by Clara Albert. Find the presentations & prerecorded demos on Zenodo. The recording will be available very soon. expands, EOSC, data services, FAIR, VISA, PaN portal
Interferences, form factor and grating intensity

Simple python script that plots the interferences, form factor and intensity as a function of the observation angle.

Keywords: grating, diffraction, optics

Interferences, form factor and grating intensity https://pan-training.eu/zenodomaterials/interferences-form-factor-and-grating-intensity Simple python script that plots the interferences, form factor and intensity as a function of the observation angle. grating, diffraction, optics
UmbrellaID Workshop: Keycloak

This one day training is dedicated to the PaN community IT people that want to enable community AAI for their users. At the end of the training it is expected that you understand what UmbrellaID and the EOSC AAI federation is. A hands on session shall demonstrate how to integrate your services...

Keywords: UmbrellaID

Resource type: slides, video

UmbrellaID Workshop: Keycloak https://pan-training.eu/materials/umbrellaid-workshop-keycloak This one day training is dedicated to the PaN community IT people that want to enable community AAI for their users. At the end of the training it is expected that you understand what UmbrellaID and the EOSC AAI federation is. A hands on session shall demonstrate how to integrate your services with UmbrellaID using Keycloak. If you want to actively participate in the hands on session, you need to have your own Keycloak installation, see the following checklist. If you don't have that, you can still participate in the workshop and also take part in the hands on session as an observer. Checklist for the hands on session: - An installation of Keycloak - Internet access from the host where they have installed Keycloak (ideally direct access, but HTTP proxy and reverse HTTP proxy are also valid) - DNS resolution for the host with Keycloak installed should be in place and should be identical from everywhere (I.E. the machine should be referenced with the same domain name from the RI/lab intranet and public internet network) - A valid X509 server certificate The session recordings can be found here: 1. https://umbrellaid.org/zoom/2022-05-03-UmbrellaID-Workshop-Session-1.mp4 2. https://umbrellaid.org/zoom/2022-05-03-UmbrellaID-Workshop-Session-2.mp4 UmbrellaID PaN Community
Containerized Serial Crystallography “CrystFEL” VISA workflow

Experiments generate up to 150 TB per day of data saved at the measurement facility. Such large datasets are impractical for users to take home. Subsequent analysis needs to be performed remotely making it attractive for deployment as a cloud-like use case. Involving EOSC in the analysis and...

Scientific topics: crystallography

Keywords: CrystFEL, Serial crystallography, pulsed X-ray beam, VISA

Resource type: workflow

Containerized Serial Crystallography “CrystFEL” VISA workflow https://pan-training.eu/materials/containerized-serial-crystallography-crystfel-visa-workflow Experiments generate up to 150 TB per day of data saved at the measurement facility. Such large datasets are impractical for users to take home. Subsequent analysis needs to be performed remotely making it attractive for deployment as a cloud-like use case. Involving EOSC in the analysis and re-use of this data is an appropriate use case. Serial crystallography is a beam-line technique for collecting information on the structure of a protein without growing large protein crystals. Instead, a large number of small protein crystals are held in a pulsed X-ray beam. In a second step, the series of produced images are used to reconstruct a precise 3-D image of the protein structure. Serial crystallography is the preferred technique for obtaining diffraction data of proteins at room temperature, where radiation damage from the X-ray beam starts rapidly. The standard software for analysing serial crystallography is “CrystFEL”. The proposed workflow was rendered in a standard fashion, which would allow it to be easily adopted by arbitrary systems or also other containerized applications. The only requirements are an Apptainer installation on the system and a Docker or Singularity/Apptainer image of the application, as well as an adjustment of the configuration file for the wrapper script. crystallography CrystFEL, Serial crystallography, pulsed X-ray beam, VISA research data scientist scientific
ETH Lib4RI: Research Data Management – The Basics

Research data management best practices in the ETH Lib4RI, the Library for the Research Institutes within the ETH Domain: Eawag, Empa, PSI & WSL

Keywords: data catalogue, data management, metadata, SciCat

Resource type: slides

ETH Lib4RI: Research Data Management – The Basics https://pan-training.eu/materials/eth-lib4ri-research-data-management-the-basics Research data management best practices in the ETH Lib4RI, the Library for the Research Institutes within the ETH Domain: Eawag, Empa, PSI & WSL data catalogue, data management, metadata, SciCat research scientists postdocs PhD students ExPaNDS and PaNOSC project members PaN users PaN Community researchers
Active DMPs for Photon and Neutron RIs

This deliverable envisions an integrated aDMP system which supports the (semi-) automated generation of DMPs by maximising reuse of information generated during the research life-cycle and also aiming to support the scientists and other stakeholders by supporting information transfer....

Keywords: expands, wp2-ExPaNDS, DMP, data management plan, data management

Resource type: Document

Active DMPs for Photon and Neutron RIs https://pan-training.eu/materials/active-dmps-for-photon-and-neutron-ris This deliverable envisions an integrated aDMP system which supports the (semi-) automated generation of DMPs by maximising reuse of information generated during the research life-cycle and also aiming to support the scientists and other stakeholders by supporting information transfer. Therefore, a data model for aDMPs focusing on the integration of information that exists before a proposal is submitted and its life-cycle integration is introduced. It relates the data model also to the template created in PaNOSC. expands, wp2-ExPaNDS, DMP, data management plan, data management PaN Community
Self-evaluation Photon and Neutron RIs for FAIR data certification

This ExPaNDS project deliverable describes a FAIR self-assessment undertaken by the ten ExPaNDS partner Photon and Neutron Research Infrastructures (PaN RIs) over the three-month period July – September 2022. After reviewing selected examples of existing FAIR evaluation frameworks designed to...

Keywords: FAIR, metadata, expands, European Photon and Neutron facilities , wp2-ExPaNDS

Resource type: Document

Self-evaluation Photon and Neutron RIs for FAIR data certification https://pan-training.eu/materials/self-evaluation-photon-and-neutron-ris-for-fair-data-certification This ExPaNDS project deliverable describes a FAIR self-assessment undertaken by the ten ExPaNDS partner Photon and Neutron Research Infrastructures (PaN RIs) over the three-month period July – September 2022. After reviewing selected examples of existing FAIR evaluation frameworks designed to enable assessment at different levels (dataset, repository, and organisation), the report describes the evaluation approach adopted for the ExPaNDS FAIR self-assessment. As no existing framework met our specific need to focus on FAIR workflows and processes in PaN RIs, it was necessary to select, combine, and adapt existing frameworks. Supported by four underlying guiding principles, our approach drew heavily on the FAIR Principles, the RDA FAIR Data Maturity Model, and FAIRsFAIR’s CoreTrustSeal+FAIRenabling framework. Post-evaluation feedback from ExPaNDS partners indicated that they found the FAIR self-assessment a useful and valuable exercise for understanding current levels of FAIRness at their facilities and for articulating what implementations they have in progress or planned to support FAIR in future. A key output of the ExPaNDS FAIR evaluation is the collected self-assessment reports from the ten partner facilities. These reports are published openly and in full as part of the deliverable. In addition, the self-assessments are supplemented with some high-level observations on the state of the FAIR journey across the ExPaNDS facilities. FAIR, metadata, expands, European Photon and Neutron facilities , wp2-ExPaNDS PaN Community
PaNOSC + ExPaNDS outcomes boosting Interoerability Data and Services for Photon and Neutron (PaN) Science / EOSC Symposium 2022 plenary

EOSC Symposium 2022 presentation by Andy Gotz: PaNOSC + ExPaNDS outcomes boosting Interoerability Data and Services for Photon and Neutron (PaN) Science.

Keywords: expands, PaNOSC

Resource type: video

PaNOSC + ExPaNDS outcomes boosting Interoerability Data and Services for Photon and Neutron (PaN) Science / EOSC Symposium 2022 plenary https://pan-training.eu/materials/panosc-expands-outcomes-boosting-interoerability-data-and-services-for-photon-and-neutron-pan-science-eosc-symposium-2022-plenary EOSC Symposium 2022 presentation by Andy Gotz: PaNOSC + ExPaNDS outcomes boosting Interoerability Data and Services for Photon and Neutron (PaN) Science. expands, PaNOSC PaN Community
Joint Public Session ExPaNDS/PaNOSC on metadata catalogues (SciCat implementation) and future perspectives

Presentations from public joint WP3 Meeting for ExPaNDS and PaNOSC, which took place in hybrid format from SOLEIL (France) and via Zoom on the 3rd November 2022. A recording of the event can be found on the ExPaNDS website: https://expands.eu/presentations/ Video recording (direct link to...

Keywords: expands, PaNOSC, open data, wp3-ExPaNDS

Resource type: slides

Joint Public Session ExPaNDS/PaNOSC on metadata catalogues (SciCat implementation) and future perspectives https://pan-training.eu/materials/work-package-3-public-meeting Presentations from public joint WP3 Meeting for ExPaNDS and PaNOSC, which took place in hybrid format from SOLEIL (France) and via Zoom on the 3rd November 2022. A recording of the event can be found on the ExPaNDS website: https://expands.eu/presentations/ Video recording (direct link to vimeo) will be available soon. expands, PaNOSC, open data, wp3-ExPaNDS data managers
Full-field Tomography at PSI

This workflow has some details on the instrument the data is produced from (TOMCAT beamline) and the infrastructure PSI has concerning their data. If you are more interested in the science and want to reproduce the data and not bother with the surrounding details/context, please refer to the...

Keywords: synchrotron, imaging, Jupyter notebooks, Python, Pulmonary arterial hypertension

Resource type: workflow

Full-field Tomography at PSI https://pan-training.eu/materials/full-field-tomography-at-psi This workflow has some details on the instrument the data is produced from (TOMCAT beamline) and the infrastructure PSI has concerning their data. If you are more interested in the science and want to reproduce the data and not bother with the surrounding details/context, please refer to the Pulmonary arterial hypertension research workflow. Full-field Tomography at PSI Tomography datasets often present large volumes (100 GBs - few TBs) difficult to compress and transfer. The tomographic reconstruction is highly demanding on compute (GPU) and storage resources for the intermediate and/or final result. In addition, the optional image segmentation step may be demanding on computer memory. The offline analysis (after experiment) could be performed remotely by users at home making it attractive for deployment as a cloud-like use case. Finally, this technique is applied at many facilities and in different scientific domains - therefore a portable result is more useful. This entire process is illustrated with a typical experiment. synchrotron, imaging, Jupyter notebooks, Python, Pulmonary arterial hypertension research data scientist life scientists