Training materials on scientific Python programming and silx libraries.
This repository contains some training materials on scientific Python programming and silx libraries.
General topics:
* Introduction to Python and numpy
* Software engineering tools and tips for Python
silx trainings:
* Features of the silx toolkit
* Introduction to Fable Input/Output...
Keywords: Python, Silx, data analysis, data reduction, data visualisation
Training materials on scientific Python programming and silx libraries.
https://github.com/silx-kit/silx-training
https://pan-training.eu/materials/training-materials-on-scientific-python-programming-and-silx-libraries
This repository contains some training materials on scientific Python programming and silx libraries.
General topics:
* Introduction to Python and numpy
* Software engineering tools and tips for Python
silx trainings:
* Features of the silx toolkit
* Introduction to Fable Input/Output (aka. fabio) library"
Python, Silx, data analysis, data reduction, data visualisation
How to mint a DOI
How to create a DOI for a specific set of datasets using the ESRF data portal.
Keywords: doi, data management, data object identifier, mint, dataset, data management, open data, Open Science, ESRF data portal
How to mint a DOI
https://www.youtube.com/watch?v=dPeN855-Mu4
https://pan-training.eu/materials/how-to-mint-a-doi
How to create a DOI for a specific set of datasets using the ESRF data portal.
doi, data management, data object identifier, mint, dataset, data management, open data, Open Science, ESRF data portal
How to share data and logbook with collaborators
How to share data and logbook with collaborators easily
Keywords: data management, open data, Open Science, logbook, sharing, ESRF data portal
How to share data and logbook with collaborators
https://www.youtube.com/watch?v=FDUFPpnllxE
https://pan-training.eu/materials/how-to-share-data-and-logbook-with-collaborators
How to share data and logbook with collaborators easily
data management, open data, Open Science, logbook, sharing, ESRF data portal
Tomwer – add a python script
Tutorial on how user can add their own processing into the workflow through a python script (advanced usage).
Scientific topics: tomography
Keywords: tomography, tomotools, tomwer, nabu, Python, canvas
Resource type: video
Tomwer – add a python script
https://www.youtube.com/watch?v=VGv628AIgn8
https://pan-training.eu/materials/tomwer-add-a-python-script
Tutorial on how user can add their own processing into the workflow through a python script (advanced usage).
tomography
tomography, tomotools, tomwer, nabu, Python, canvas
TANGO tutorials
Documentation and tutorials to understand what Tango Controls is, guide your first steps as a user, developer or administrator of Tango.
Keywords: synchrotron control, TANGO, c++, Python, tango-controls, arduino, scada
Resource type: documenation
TANGO tutorials
https://tango-controls.readthedocs.io/en/latest/tutorials-and-howtos/tutorials/index.html
https://pan-training.eu/materials/tango-tutorials
Documentation and tutorials to understand what Tango Controls is, guide your first steps as a user, developer or administrator of Tango.
synchrotron control, TANGO, c++, Python, tango-controls, arduino, scada
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
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
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
Final recommendations for FAIR Photon and Neutron Data Management
The present deliverable pursues the work initiated in ExPaNDS deliverable 2.2, which established a common metadata framework for FAIR data generated in Photon and Neutron (PaN) facilities. The modalities of implementation of this framework across facilities are examined and current practices and...
Keywords: expands, wp2-ExPaNDS, FAIR, data management
Resource type: Document
Final recommendations for FAIR Photon and Neutron Data Management
https://zenodo.org/record/6821676#.YwiWdnHP02w
https://pan-training.eu/materials/final-recommendations-for-fair-photon-and-neutron-data-management
The present deliverable pursues the work initiated in ExPaNDS deliverable 2.2, which established a common metadata framework for FAIR data generated in Photon and Neutron (PaN) facilities. The modalities of implementation of this framework across facilities are examined and current practices and tools for metadata capture, storage and exposure are highlighted. This work is also the occasion to examine the commonalities of the framework with other initiatives developed inside and outside ExPaNDS such as the common search API, the data catalogues (ExPaNDS WP3), the EOSC discovery platforms B2FIND and OpenAire as well as the NeXus data format. It also provides the reader with guidelines on current tools and schemata available to record provenance and digital preservation information. The essence of these discussions is summarised as a list of practical recommendations at the end.
expands, wp2-ExPaNDS, FAIR, data management
PaN Community
Workshop on Metadata Catalogues
Presentations from the Workshop on Metadata Catalogues, which took place virtually via Zoom on the 4th April 2022.
Keywords: data catalogue, SciCat, ICAT, expands, panet, PaNOSC, metadata, data management, data processing, wp3-ExPaNDS
Resource type: slides, video
Workshop on Metadata Catalogues
https://zenodo.org/record/6414117
https://pan-training.eu/materials/workshop-on-metadata-catalogues
Presentations from the Workshop on Metadata Catalogues, which took place virtually via Zoom on the 4th April 2022.
data catalogue, SciCat, ICAT, expands, panet, PaNOSC, metadata, data management, data processing, wp3-ExPaNDS
data curator
data managers
research data engineer
ExPaNDS and PaNOSC project members
PaN users
PaN Community
Outreach videos about experiments done at ALBA
Here you will find a series of videos about the different applications of synchrotron light. Videos are in Spanish and Catalan, although subtitles are available in English, Catalan and Spanish.
Its aim is to transmit in a simple and understandable way a selection of the applications that can...
Keywords: synchrotron, synchrotron light, applications
Resource type: video
Outreach videos about experiments done at ALBA
https://www.cells.es/en/outreach/videos
https://pan-training.eu/materials/outreach-videos-about-experiments-done-at-alba
Here you will find a series of videos about the different applications of synchrotron light. Videos are in Spanish and Catalan, although subtitles are available in English, Catalan and Spanish.
Its aim is to transmit in a simple and understandable way a selection of the applications that can have the synchrotron light in different scientific fields: health, food, environment, cultural heritage, etc.
These videos are part of the project FCT-15-9828 "Bringing science to society – Outreach science program of the ALBA Synchrotron", funded by the Spanish Foundation for Science and Technology (FECYT) - Ministry of Economy and Competitiveness and the Foundation Obra Social "la Caixa".
synchrotron, synchrotron light, applications
general public
Tour of MAX IV accelerators with professor Sverker Werin
Join us in the tour of MAX IV Laboratory's accelerators hosted by Sverker Werin, professor in accelerator physics at Lund University and MAX IV.
The electron guns 00:24
Along the linear accelerator 2:59
The bunch compressor 4:42
The 1.5 GeV ring extraction point 5:47
The modulators and...
Keywords: synchrotron, accelerator physics
Resource type: video
Tour of MAX IV accelerators with professor Sverker Werin
https://www.youtube.com/watch?v=2TJMFlkyFwc
https://pan-training.eu/materials/tour-of-max-iv-accelerators-with-professor-sverker-werin
Join us in the tour of MAX IV Laboratory's accelerators hosted by Sverker Werin, professor in accelerator physics at Lund University and MAX IV.
The electron guns 00:24
Along the linear accelerator 2:59
The bunch compressor 4:42
The 1.5 GeV ring extraction point 5:47
The modulators and klystrons 7:03
In the 3.0 GeV storage ring 8:13
The undulators in the 3.0 GeV rings 10:50
The start of the photon beam 11:57
Topping up energy in the storage ring 12:42
In the MAX IV accelerator exhibition 13:39
synchrotron, accelerator physics
PaN Community
beamline users
Learning pack: The synchrotron and its lights
The machine and beamlines, optical devices, magnetism vacuum and information about the analytic techniques applied on a synchrotron and through examples of studies carried out at the synchrotron SOLEIL.
Scientific topics: extended x-ray absorption fine structure, absorption spectroscopy
Keywords: synchrotron, optics, monochromators, magnetic fields, ultra-high vacuum, applications, xanes & exafs
Resource type: Document
Learning pack: The synchrotron and its lights
https://www.synchrotron-soleil.fr/mallettes-pedagogiques/the-synchrotron-and-its-light
https://pan-training.eu/materials/learning-pack-the-synchrotron-and-its-lights
The machine and beamlines, optical devices, magnetism vacuum and information about the analytic techniques applied on a synchrotron and through examples of studies carried out at the synchrotron SOLEIL.
extended x-ray absorption fine structure
absorption spectroscopy
synchrotron, optics, monochromators, magnetic fields, ultra-high vacuum, applications, xanes & exafs
general public
masters students
Learning pack: Optics
What optic devices are used to direct light, concentrate it and select a wavelength?
Do they all involve the same technology?
An educational introduction to optical instruments.
Poster "Optical instruments suited to the light of the SOLEIL"
Keywords: synchrotron, optical instruments
Resource type: Poster
Learning pack: Optics
https://www.synchrotron-soleil.fr/sites/default/files/education/poster-optical-instruments.pdf
https://pan-training.eu/materials/learning-pack-optics
What optic devices are used to direct light, concentrate it and select a wavelength?
Do they all involve the same technology?
An educational introduction to optical instruments.
Poster "Optical instruments suited to the light of the SOLEIL"
synchrotron, optical instruments
general public
Synchrotron, a light source for research
PART 1:
SOLEIL, a light source for research
How does a synchrotron work? Who comes here to perform experiments? Find some answers in this illustrated video.
PART 2:
The lights of SOLEIL
What lights are used at SOLEIL? Why such a diversity? Find some answers in this illustrated video, very...
Keywords: synchrotron, Soleil
Resource type: video
Synchrotron, a light source for research
https://www.youtube.com/watch?v=GwD5bZCJ1T8
https://pan-training.eu/materials/synchrotron-a-light-source-for-research
PART 1:
SOLEIL, a light source for research
How does a synchrotron work? Who comes here to perform experiments? Find some answers in this illustrated video.
PART 2:
The lights of SOLEIL
What lights are used at SOLEIL? Why such a diversity? Find some answers in this illustrated video, very accessible and didactic.
PART 3:
When light explores matter
What happens when light is shone at a sample? What techniques and applications are available at SOLEIL? Find some answers in this illustrated video, very accessible and didactic.
Find more videos on our website https://www.synchrotron-soleil.fr/en/videos
synchrotron, Soleil
general public
FTIR Microscopy with Synchrotron Radiation
FTIR Microscopy with Synchrotron Radiation by Dr. Lisa Vaccari from CERIC’s Italian Partner Facility, Elettra Synchrotron in Trieste
Keywords: synchrotron, Elettra synchrotron, synchrotron beamline, FTIR Microscopy, Photon science
Resource type: video
FTIR Microscopy with Synchrotron Radiation
https://youtu.be/t1cVzrXj7go
https://pan-training.eu/materials/ftir-microscopy-with-synchrotron-radiation
FTIR Microscopy with Synchrotron Radiation by Dr. Lisa Vaccari from CERIC’s Italian Partner Facility, Elettra Synchrotron in Trieste
synchrotron, Elettra synchrotron, synchrotron beamline, FTIR Microscopy, Photon science
PaN Community
PaN users
PhD students
Soft X-ray Imaging and XRF
Soft X-ray Imaging and XRF by Dr. Alessandra Gianoncelli from CERIC’s Italian Partner Facility, Elettra Synchrotron in Trieste
Keywords: Soft X-ray Imaging, X-ray fluorescence, XRF, synchrotron, synchrotron beamline, Elettra synchrotron, Photon science
Resource type: video
Soft X-ray Imaging and XRF
https://youtu.be/RoZYrVcXG5Y
https://pan-training.eu/materials/soft-x-ray-imaging-and-xrf
Soft X-ray Imaging and XRF by Dr. Alessandra Gianoncelli from CERIC’s Italian Partner Facility, Elettra Synchrotron in Trieste
Soft X-ray Imaging, X-ray fluorescence, XRF, synchrotron, synchrotron beamline, Elettra synchrotron, Photon science
PaN Community
PaN users
PhD students
Introduction to Powder Diffraction
Introduction to Powder Diffraction by Dr. Jasper Plaisier from CERIC’s Italian Partner Facility, Elettra Synchrotron in Trieste
Scientific topics: powder diffraction
Keywords: Powder Diffraction, synchrotron, Photon science, synchrotron beamline, Elettra synchrotron
Resource type: video
Introduction to Powder Diffraction
https://youtu.be/iQOIbh0W__U
https://pan-training.eu/materials/introduction-to-powder-diffraction
Introduction to Powder Diffraction by Dr. Jasper Plaisier from CERIC’s Italian Partner Facility, Elettra Synchrotron in Trieste
powder diffraction
Powder Diffraction, synchrotron, Photon science, synchrotron beamline, Elettra synchrotron
PaN Community
PaN users
PhD students
X-ray Diffraction: Macromolecular Crystallography
X-ray Diffraction: Macromolecular Crystallography by Dr. Annie Heroux from CERIC’s Italian Partner Facility, Elettra Synchrotron in Trieste
Keywords: X-ray Diffraction, Macromolecular Crystallography, synchrotron, Photon science, synchrotron beamline, Elettra synchrotron
X-ray Diffraction: Macromolecular Crystallography
https://youtu.be/Yuj-s4UByaA
https://pan-training.eu/materials/x-ray-diffraction-macromolecular-crystallography
X-ray Diffraction: Macromolecular Crystallography by Dr. Annie Heroux from CERIC’s Italian Partner Facility, Elettra Synchrotron in Trieste
X-ray Diffraction, Macromolecular Crystallography, synchrotron, Photon science, synchrotron beamline, Elettra synchrotron
PaN Community
PaN users
PhD students
Introduction to X-ray Imaging
Introduction to X-ray Imaging by Dr. Giuliana Tromba from CERIC’s Italian Partner Facility, Elettra Synchrotron in Trieste
Scientific topics: x-ray imaging
Keywords: X-ray Imaging, Photon science, synchrotron, synchrotron beamline, Elettra synchrotron
Resource type: video
Introduction to X-ray Imaging
https://youtu.be/GVjuAvqLz0w
https://pan-training.eu/materials/introduction-to-x-ray-imaging
Introduction to X-ray Imaging by Dr. Giuliana Tromba from CERIC’s Italian Partner Facility, Elettra Synchrotron in Trieste
x-ray imaging
X-ray Imaging, Photon science, synchrotron, synchrotron beamline, Elettra synchrotron
PaN users
PaN Community
PhD students
Introduction to X-ray Spectroscopy & Microscopy
Introduction to X-ray Spectroscopy & Microscopy by Dr. Andrea Locatelli from CERIC’s Italian Partner Facility, Elettra Synchrotron in Trieste
Keywords: X-ray Spectroscopy, X-ray Microscopy, Photon science, synchrotron, synchrotron beamline, Elettra synchrotron
Resource type: video
Introduction to X-ray Spectroscopy & Microscopy
https://youtu.be/EOlvBqDURDU
https://pan-training.eu/materials/introduction-to-x-ray-spectroscopy-microscopy
Introduction to X-ray Spectroscopy & Microscopy by Dr. Andrea Locatelli from CERIC’s Italian Partner Facility, Elettra Synchrotron in Trieste
X-ray Spectroscopy, X-ray Microscopy, Photon science, synchrotron, synchrotron beamline, Elettra synchrotron
PaN users
PaN Community
PhD students
Introduction to X/N Matter Interactions
Introduction to X/N Matter Interactions by Dr. Maya Kisknova from CERIC’s Italian Partner Facility, Elettra Synchrotron in Trieste
Keywords: synchrotron, Elettra synchrotron, Photon science
Resource type: video
Introduction to X/N Matter Interactions
https://youtu.be/WRrmKK8rHw4
https://pan-training.eu/materials/introduction-to-x-n-matter-interactions
Introduction to X/N Matter Interactions by Dr. Maya Kisknova from CERIC’s Italian Partner Facility, Elettra Synchrotron in Trieste
synchrotron, Elettra synchrotron, Photon science
PaN Community
PaN users
PhD students
Introduction to Soft X-ray Transmission and Emission Microscope, TwinMic at Elettra Sincrotrone Trieste
Introduction to the TwinMic Beamline:
Soft X-ray Transmission and Emission Microscope at the CERIC Italian partner facility, Elettra Sincrotrone Trieste
---TwinMic beamline webpage in the CERIC website:...
Keywords: soft X-ray Microscopy, synchrotron, Central European Research Infrastructure Consortium, CERIC, synchrotron beamline, microscopy, electrochemistry, battery research, Heritage Science, Elettra synchrotron, Elettra Sincrotrone Trieste, life sciences, microscope
Resource type: video
Introduction to Soft X-ray Transmission and Emission Microscope, TwinMic at Elettra Sincrotrone Trieste
https://youtu.be/Z7bo5jgOhWU
https://pan-training.eu/materials/introduction-to-soft-x-ray-transmission-and-emission-microscope-twinmic-at-elettra-sincrotrone-trieste
Introduction to the TwinMic Beamline:
Soft X-ray Transmission and Emission Microscope at the CERIC Italian partner facility, Elettra Sincrotrone Trieste
---TwinMic beamline webpage in the CERIC website: https://www.ceric-eric.eu/lab-instrument/soft-x-ray-transmission-and-emission-microscope/
---TwinMic beamline webpage in the Elettra website: https://www.elettra.trieste.it/elettra-beamlines/twinmic.html
soft X-ray Microscopy, synchrotron, Central European Research Infrastructure Consortium, CERIC, synchrotron beamline, microscopy, electrochemistry, battery research, Heritage Science, Elettra synchrotron, Elettra Sincrotrone Trieste, life sciences, microscope
researchers
scientists
PhD students
chemists
physicists
biologists
The FAIR Experiment
Video recording of the workshop exploring the FAIR Experiment at PaN facilities (02/10/2020)
Keywords: FAIR, research data, data management, metadata, wp2-ExPaNDS
Resource type: video
The FAIR Experiment
https://vimeo.com/493767139
https://pan-training.eu/materials/the-fair-experiment
Video recording of the workshop exploring the FAIR Experiment at PaN facilities (02/10/2020)
FAIR, research data, data management, metadata, wp2-ExPaNDS
facility staff
instrument scientist
Python Laser Image Visualization
Tool showing pictures from different cameras (directories) in a grid and a stepwise counter-based scroll functionality. Most of the layout and (future) filter options are defined by command line to allow an easy integration into an workflow based on CWL, OWL (or Knime). In future developments...
Keywords: Python, Laser, Visualization, Cameras, Laser Ion Acceleration, Qt5
Resource type: software, git
Python Laser Image Visualization
https://gitlab.hzdr.de/fwcc/data-management/user-project-documentation/laserviztool
https://pan-training.eu/materials/python-laser-image-visualization
Tool showing pictures from different cameras (directories) in a grid and a stepwise counter-based scroll functionality. Most of the layout and (future) filter options are defined by command line to allow an easy integration into an workflow based on CWL, OWL (or Knime). In future developments most of the parameters can be changed interactive and saved to a json file which can be used to describe the next workflow inputs, so that an interactive workflow development is possible.
Python, Laser, Visualization, Cameras, Laser Ion Acceleration, Qt5
PaN Community
Photon Community