Tomwer: Slice stack standalone
How to display a set of slices from the standalone application
Scientific topics: tomography
Keywords: tomography, tomotools, tomwer, nabu, volume, projections, NXtomo
Resource type: video
Tomwer: Slice stack standalone
https://www.youtube.com/watch?v=4xpvQB2DIPk
https://pan-training.eu/materials/tomwer-slice-stack-standalone
How to display a set of slices from the standalone application
tomography
tomography, tomotools, tomwer, nabu, volume, projections, NXtomo
Tomwer: Slice stack from canvas
How to display a set of slice from the orange canvas
Scientific topics: tomography
Keywords: tomography, tomotools, tomwer, nabu, volume, projections, NXtomo, canvas
Resource type: video
Tomwer: Slice stack from canvas
https://www.youtube.com/watch?v=3X9ePy8eSg4
https://pan-training.eu/materials/tomwer-slice-stack-from-canvas
How to display a set of slice from the orange canvas
tomography
tomography, tomotools, tomwer, nabu, volume, projections, NXtomo, canvas
NXtomo stitching
tutorial on how to stitch NXtomos (projections) together.
Scientific topics: tomography
Keywords: tomography, tomotools, tomwer, nabu, stitching, NXtomo, projections
Resource type: video
NXtomo stitching
https://www.youtube.com/watch?v=t-VinnwtIfw
https://pan-training.eu/materials/nxtomo-stitching
tutorial on how to stitch NXtomos (projections) together.
tomography
tomography, tomotools, tomwer, nabu, stitching, NXtomo, projections
Tomwer: Z stitching of reconstructed volumes
Tutorials on how to stitch volumes reconstructed with nabu that have their positions along axis 0 (aka z) changing. Usually called a z-serie.
tomotools
Scientific topics: tomography
Keywords: tomography, tomotools, tomwer, nabu, stitching, volume
Resource type: video
Tomwer: Z stitching of reconstructed volumes
https://www.youtube.com/watch?v=Yhrde42Xxxs
https://pan-training.eu/materials/tomwer-z-stitching-of-reconstructed-volumes
Tutorials on how to stitch volumes reconstructed with nabu that have their positions along axis 0 (aka z) changing. Usually called a z-serie.
tomotools
tomography
tomography, tomotools, tomwer, nabu, stitching, volume
Tomwer: Cancelling task
short example on how to cancel a on-going or pending task from the 'object supervisor'
Scientific topics: tomography
Keywords: tomography, tomotools, tomwer, nabu, task cancellation, canvas
Resource type: video
Tomwer: Cancelling task
https://www.youtube.com/watch?v=MTMtw4oKV0I
https://pan-training.eu/materials/tomwer-cancelling-task
short example on how to cancel a on-going or pending task from the 'object supervisor'
tomography
tomography, tomotools, tomwer, nabu, task cancellation, canvas
Tomwer: Axis widget
simple demo of the 'axis widget' used to determine the center of rotation be fore slice reconstruction
Scientific topics: tomography
Keywords: tomography, tomotools, tomwer, nabu, center of rotation, axis, canvas
Resource type: video
Tomwer: Axis widget
https://www.youtube.com/watch?v=sc3Pmg7zWHQ
https://pan-training.eu/materials/tomwer-axis-widget
simple demo of the 'axis widget' used to determine the center of rotation be fore slice reconstruction
tomography
tomography, tomotools, tomwer, nabu, center of rotation, axis, canvas
Access tomotools from visa.esrf.fr
Short description on how to:
- connect to visa.esrf.fr (the ESRF's Virtual Research Environment)
- create an instance (if needed)
- load 'tomotools' module
- run a simple reconstruction with nabu from CLI
- display the reconstruction with silx view
- unload the module
Scientific topics: tomography
Keywords: tomography, tomotools, nabu, VISA
Resource type: video
Access tomotools from visa.esrf.fr
https://www.youtube.com/watch?v=nERMMj3y64M
https://pan-training.eu/materials/access-tomotools-from-visa-esrf-fr
Short description on how to:
- connect to visa.esrf.fr (the ESRF's Virtual Research Environment)
- create an instance (if needed)
- load 'tomotools' module
- run a simple reconstruction with nabu from CLI
- display the reconstruction with silx view
- unload the module
tomography
tomography, tomotools, nabu, VISA
Tomwer – semi-automated delta/beta research
"Tutorial to explain how to use the `sadeltabeta` widget.
This widget is dedicated to research of delta / beta parameter. And use the same structure/mecanism as the `saaxis` widget and offer the same features. This video only show the 'interactive' mode but a 'fully automated' mode exists (see...
Scientific topics: tomography
Keywords: tomography, tomotools, tomwer, nabu, Paganin, canvas
Resource type: video
Tomwer – semi-automated delta/beta research
https://www.youtube.com/watch?v=A8bZtEwLF7I
https://pan-training.eu/materials/tomwer-semi-automated-delta-beta-research
"Tutorial to explain how to use the `sadeltabeta` widget.
This widget is dedicated to research of delta / beta parameter. And use the same structure/mecanism as the `saaxis` widget and offer the same features. This video only show the 'interactive' mode but a 'fully automated' mode exists (see video done for saaxis if necessary.)"
tomography
tomography, tomotools, tomwer, nabu, Paganin, canvas
How to edit NXtomo metadata
In this video we will show show you how to edit NXtomo metadata such as beam energy or sample / detector distance.
Scientific topics: tomography
Keywords: tomography, tomotools, tomwer, nabu, NeXus, NXtomo, edition, canvas
Resource type: video
How to edit NXtomo metadata
https://www.youtube.com/watch?v=KwwCYXnP3YI
https://pan-training.eu/materials/how-to-edit-nxtomo-metadata
In this video we will show show you how to edit NXtomo metadata such as beam energy or sample / detector distance.
tomography
tomography, tomotools, tomwer, nabu, NeXus, NXtomo, edition, canvas
Tomwer – semi-automated center of rotation
"Tutorial to explain how to use the `saaxis` widget.
This widget is dedicated to research of center of rotation which is a common bottleneck when reconstructing tomographic dataset.
From it user can launch reconstruction for a serie of center of rotation and the same nabu reconstruction...
Scientific topics: tomography
Keywords: tomography, tomotools, tomwer, nabu, center of rotation, axis, canvas
Resource type: video
Tomwer – semi-automated center of rotation
https://www.youtube.com/watch?v=G9G55lGuDeA
https://pan-training.eu/materials/tomwer-semi-automated-center-of-rotation
"Tutorial to explain how to use the `saaxis` widget.
This widget is dedicated to research of center of rotation which is a common bottleneck when reconstructing tomographic dataset.
From it user can launch reconstruction for a serie of center of rotation and the same nabu reconstruction settings.
Once reconstructed it compute scores on those reconstruction (like standard deviation, total variation...) to help users find the best value.
Here we show how this process can be automatize"
tomography
tomography, tomotools, tomwer, nabu, center of rotation, axis, canvas
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
Tomwer: How to use 'edf2nx' (convert EDF acquisition to NXtomo)
In this video we explain how to convert EDF acquisitions to NXtomos and the different options related to it.
Scientific topics: tomography
Keywords: tomography, tomotools, tomwer, nabu, spec, EDF, NXtomo, NeXus, canvas
Resource type: video
Tomwer: How to use 'edf2nx' (convert EDF acquisition to NXtomo)
https://www.youtube.com/watch?v=Xzb_WDiDNsk
https://pan-training.eu/materials/tomwer-how-to-use-edf2nx-convert-edf-acquisition-to-nxtomo
In this video we explain how to convert EDF acquisitions to NXtomos and the different options related to it.
tomography
tomography, tomotools, tomwer, nabu, spec, EDF, NXtomo, NeXus, canvas
Tomwer: How to define a volume from a drag and drop
"Explain how user can simply define a volume by a single drag and drop.
* In the case of 'file based volume (like HDF5)' user must drag the 'master file'
* In the case of 'folder baed volume (like EDF, JP2K...)' user must drag the 'master folder'"
Scientific topics: tomography
Keywords: tomography, tomotools, tomwer, nabu, volume, canvas
Resource type: video
Tomwer: How to define a volume from a drag and drop
https://www.youtube.com/watch?v=R2jJrIZlGY8
https://pan-training.eu/materials/tomwer-how-to-define-a-volume-from-a-drag-and-drop
"Explain how user can simply define a volume by a single drag and drop.
* In the case of 'file based volume (like HDF5)' user must drag the 'master file'
* In the case of 'folder baed volume (like EDF, JP2K...)' user must drag the 'master folder'"
tomography
tomography, tomotools, tomwer, nabu, volume, canvas
How to edit NXtomo image key
"In this video we show you one dedicated interface to edit `image_key` of a specific NXtomo.
This can allow user to ignore some frames (if image_key is set to zero) or fix some wrong image key."
Scientific topics: tomography
Keywords: tomography, tomotools, tomwer, nabu, NXtomo, NeXus, edition, image key
Resource type: video
How to edit NXtomo image key
https://www.youtube.com/watch?v=4yrEBrAmwtY
https://pan-training.eu/materials/how-to-edit-nxtomo-image-key
"In this video we show you one dedicated interface to edit `image_key` of a specific NXtomo.
This can allow user to ignore some frames (if image_key is set to zero) or fix some wrong image key."
tomography
tomography, tomotools, tomwer, nabu, NXtomo, NeXus, edition, image key
How to use projections from an NXtomo to be used as (reduced) flats or darks
"In this video we show how to use frames contains in an NXtomo as flats then as reduced flats.
The same process works for other manipulation (as creating reduced darks)"
Scientific topics: tomography
Keywords: tomography, tomotools, tomwer, nabu, NXtomo, NeXus, reduced frames, edition, canvas
Resource type: video
How to use projections from an NXtomo to be used as (reduced) flats or darks
https://www.youtube.com/watch?v=vJOo0rHHUYk
https://pan-training.eu/materials/how-to-use-projections-from-an-nxtomo-to-be-used-as-reduced-flats-or-darks
"In this video we show how to use frames contains in an NXtomo as flats then as reduced flats.
The same process works for other manipulation (as creating reduced darks)"
tomography
tomography, tomotools, tomwer, nabu, NXtomo, NeXus, reduced frames, edition, canvas
How to convert (NXtomo) projections to reduced flats and use it
On this video we explain how to use projections (from an NXtomo) as flats then use them as reduced flats with another dataset.
Scientific topics: tomography
Keywords: tomography, tomotools, tomwer, nabu, NXtomo, NeXus, reduced frames, edition, canvas
Resource type: video
How to convert (NXtomo) projections to reduced flats and use it
https://www.youtube.com/watch?v=qwmBGes9G_A
https://pan-training.eu/materials/how-to-convert-nxtomo-projections-to-reduced-flats-and-use-it
On this video we explain how to use projections (from an NXtomo) as flats then use them as reduced flats with another dataset.
tomography
tomography, tomotools, tomwer, nabu, NXtomo, NeXus, reduced frames, edition, canvas
Tomwer: Select a volume from dedicated interface
how to use the `volume selector` when you can't or don't want to do a drag and drop
Scientific topics: tomography
Keywords: tomography, tomotools, nabu, tomwer, volume, canvas
Resource type: video
Tomwer: Select a volume from dedicated interface
https://www.youtube.com/watch?v=4-RJKWlP74w
https://pan-training.eu/materials/tomwer-select-a-volume-from-dedicated-interface
how to use the `volume selector` when you can't or don't want to do a drag and drop
tomography
tomography, tomotools, nabu, tomwer, volume, canvas
Tomwer: How to copy reduced darks and flats
Explain one solution to copy existing reduced darks and flats to be used on another dataset
Scientific topics: tomography
Keywords: tomography, tomotools, tomwer, nabu, reduced frames, copy, canvas
Resource type: video
Tomwer: How to copy reduced darks and flats
https://www.youtube.com/watch?v=aBLTWmuMTcQ
https://pan-training.eu/materials/tomwer-how-to-copy-reduced-darks-and-flats
Explain one solution to copy existing reduced darks and flats to be used on another dataset
tomography
tomography, tomotools, tomwer, nabu, reduced frames, copy, canvas
Tomwer: How to cast a volume to another type
On this video we explain how user can convert a volume (like HDF5 float32) to another type (like tiff-uint8)
Scientific topics: tomography
Keywords: tomography, tomotools, tomwer, nabu, volume, casting, canvas
Resource type: video
Tomwer: How to cast a volume to another type
https://www.youtube.com/watch?v=gQRWCsyIm7U
https://pan-training.eu/materials/tomwer-how-to-cast-a-volume-to-another-type
On this video we explain how user can convert a volume (like HDF5 float32) to another type (like tiff-uint8)
tomography
tomography, tomotools, tomwer, nabu, volume, casting, canvas
"Processing tomographic data with tomwer software Step 5 - launch job on slurm"
video on how to launch some nabu job (slice / volume) reconstruction to the slurm-cluster
Scientific topics: tomography
Keywords: tomography, tomotools, tomwer, nabu, slurm, canvas
Resource type: video
"Processing tomographic data with tomwer software Step 5 - launch job on slurm"
https://www.youtube.com/watch?v=HYufV7Ya9v8
https://pan-training.eu/materials/processing-tomographic-data-with-tomwer-software-step-5-launch-job-on-slurm
video on how to launch some nabu job (slice / volume) reconstruction to the slurm-cluster
tomography
tomography, tomotools, tomwer, nabu, slurm, canvas
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
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
Cryo electron microscopy
An introduction to the Diamond Light Source cryo-electron microscope facilities.
Scientific topics: cryo x-ray microscopy
Keywords: cryo-electron tomography, single particle analysis
Resource type: video
Cryo electron microscopy
https://vimeo.com/317009040
https://pan-training.eu/materials/cryo-electron-microscopy
An introduction to the Diamond Light Source cryo-electron microscope facilities.
cryo x-ray microscopy
cryo-electron tomography, single particle analysis
PaNdata software catalogue
PaNdata software catalogue is a database of software used mainly for data analysis of neutron and photon experiments.
Scientific topics: photon and neutron technique, crystallography, imaging, macromolecular crystallography, nuclear resonant scattering, powder diffraction, ptychography, radiotherapy, small angle x-ray scattering, small angle inelastic scattering, single crystal diffraction, surface crystallography, tomography
Keywords: software, FAIR, catalogue
Resource type: tool
PaNdata software catalogue
https://software.pan-data.eu/
https://pan-training.eu/materials/pandata-software-catalogue
PaNdata software catalogue is a database of software used mainly for data analysis of neutron and photon experiments.
photon and neutron technique
crystallography
imaging
macromolecular crystallography
nuclear resonant scattering
powder diffraction
ptychography
radiotherapy
small angle x-ray scattering
small angle inelastic scattering
single crystal diffraction
surface crystallography
tomography
software, FAIR, catalogue
scientists
neutron community
Photon Community
research data scientist
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