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://www.youtube.com/watch?v=6X-hK2yuBbU
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://www.youtube.com/watch?v=53XcgiVWQy0
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://www.youtube.com/watch?v=w8k9Z2HZW8E
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://www.youtube.com/watch?v=TllM0LBAb8E
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://www.youtube.com/watch?v=OVHGzxZaZ0E
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://www.youtube.com/watch?v=ui6cA9VoVhA
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://www.youtube.com/watch?v=j0cphX3z2mM
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://www.youtube.com/watch?v=7xqT_8RWyPE
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://www.youtube.com/watch?v=QVbaBlYTFwg
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://www.silx.org/pub/integrator/doc/
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://tomotools.gitlab-pages.esrf.fr/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://www.silx.org/pub/nabu/doc/
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://berd-nfdi.github.io/BERD-reproducible-research-course/
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://osf.io/ar57z/
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://www.youtube.com/watch?v=9wCh2z8e7DI
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://www.sni-portal.de/en/user-committees/committee-research-with-neutrons/neutron-webinar/kfn-neutron-webinar-recorded-lectures
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://fs-mcp.pages.desy.de/nuclear-nexus/tutorial/tutorial.html
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://gitlab.desy.de/fs-mcp/nuclear-nexus
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://zenodo.org/record/7634045
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://zenodo.org/record/7599707
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://zenodo.org/record/7599600
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://zenodo.org/record/7598278
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://indico.psi.ch/event/12701/
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/workflows/containerized-serial-crystallography-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://www.lib4ri.ch/sites/default/files/media/documents/2023_05_PhD-Training_RDM_PSI_web.pdf
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://zenodo.org/record/7223438
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://zenodo.org/record/7246802
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://www.youtube.com/watch?v=x6MH0dj-EAQ&t=2094s
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://expands.eu/presentations/#WP3PublicMeeting
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/workflows/backup-fork-of-full-field-tomography-at-psi-wip#workflow
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