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Scientific topics: imaging  or absorption contrast imaging  or obtain 3D spatial map  or tomography  or fluorescence tomography  or obtain high resolution spat...  or microscopy  or infrared microspectroscopy  or fluorescence microscopy  or fluorescence imaging  or

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://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://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://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://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://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://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://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://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://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://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://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://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://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://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://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://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://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://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://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://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://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
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
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://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://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://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