X-ray Tomography at Synchrotron Facilities

Feb 22, 2021, 2:45 PM → Feb 26, 2021, 6:45 PM GMT

Virtual

X-ray Tomography at Synchrotron Facilities

Pipeline for data acquisition and reduction workshop

During the last few years several advances in control, detector and data analysis have been transforming the operation of tomography instrumentation at synchrotron facilities and more changes are planned as several facilities are undergoing extensive upgrades.

In this virtual workshop, organized thanks to the collaboration between the European Beamline Jockeys (BJ) and USA synchrotron communities, we would like to gather and share the experience of beamline and computational scientists directly involved with operation asking them to present the current pipeline for data acquisition and reconstruction encouraging a demo presentation.

The scheduled presentations (see the Contribution List) will focus on the operation of the beamlines for full field tomography experiments with a brief introduction of the beamline operation (up to 30 min) in most of the cases coupled with a live or recorded demo session (up to 40 min) elaborating on the details of the functions and processes carried out during an experimental session (such as sample mounting, set-up alignment, parameters selection for tomographic scans, data migration, reconstruction, conversion, storage, and/or any other steps selected by the presenters).

When possible, we would encourage a shared demo including the involvement of the software/controls developers who can provide comprehensive details and explanations.

Alexander Rack (ESRF)

Christoph Rau (Diamond)

Francesco De Carlo (APS)

Dilworth Y. Parkinson (ALS)

Lucia Mancini (Elettra)

Monday, February 22

3:00 PM → 3:20 PM Welcome address

Speakers: Francesco De Carlo (APS), Lucia Mancini (Elettra - SIncrotrone Trieste S.C.p.A., LINXS)

3:20 PM → 4:30 PM Tomography at the Advanced Photon Source

Speaker: Mark Rivers, Viktor Nikitin and Francesco De Carlo (Advanced Photon Source)

Abstract_APSfin.pdf

4:30 PM → 4:55 PM Interactive Q&A (moderator: L. Mancini)

4:55 PM → 5:10 PM Break

5:10 PM → 6:20 PM Workflows at Diamond's tomography beamlines

Typical workflows for microtomography experiments at I12, I13-2 and DIAD will be presented. I12 (53-150keV) and I13-2 (8-30keV) are suited to large and small samples respectively, and the new beamline DIAD (7-38keV) will allow simultaneous imaging and diffraction for small samples. Methods for accurate beamline alignment and stable sample mounting will be discussed, together with the optimisation of scanning parameters for various ex and in situ scenarios. Software for beamline control (EPICS), data acquisition (GDA) and reconstruction (Savu) will be presented alongside methods and policies for data migration and archiving.

Speaker: Andrew Bodey, Robert Atwood and Sharif Ahmed (Diamond Light Source)

6:20 PM → 6:50 PM Interactive Q&A (moderator: D.Y. Parkinson)

Tuesday, February 23

3:00 PM → 3:05 PM Short introduction to Day 2

3:05 PM → 3:50 PM Tomodata - a Python interface for PyHST2 at SOLEIL

At SOLEIL's tomography beamlines, tomography acquisitions are performed using the SOLEIL FlyScan continuous scanning architecture. The resulting data are reconstructed using PyHST2. In both cases, a layer of Python code has been developed to guide the user through the process, aligning samples, setting parameters, correcting artefacts, and launching reconstructions. Batch or pipeline processing are possible.
We have also put a great deal of thought into the computing hardware used for data storage, transfer, and processing, and at the PSICHE beamline this is in the process of being upgraded to its second iteration.
This presentation will demonstrate the above tomography workflow, and will explain the new computing systems. Comments, questions, and suggestions for future developments are welcomed.

Speaker: Andrew King (SOLEIL Synchrotron)

3:50 PM → 4:15 PM Interactive Q&A (moderator: C. Rau)

4:15 PM → 4:30 PM Break

4:30 PM → 5:00 PM System control and data reduction for nano-resolution spectro-tomography at SSRL

Speaker: Yijin Liu (Stanford Synchrotron Radiation Lightsource)

Abstract_SSRL.pdf

5:00 PM → 5:25 PM Interactive Q&A (moderator: F. De Carlo)

5:25 PM → 5:55 PM Multiscale monochromatic and pink-beam microCT imaging at the ESRF-ID17 biomedical beamline

Recent trends in hard X-ray biomedical microCT aim at pushing the limits in both spatial and temporal resolutions. Additionally, when functional parameters in small animal organs need to be accessed, microCT has to be performed in vivo. All these challenges necessitate intense and coherent photon beams. To address these requests, the ESRF-ID17 biomedical beamline is equipped with different setups, using either monochromatic beam in the range 30-100 keV for low-medium resolution or pink-beam with a spectrum optimized around 25-50 keV for submicron imaging.
The presentation will illustrate the different options available at ID17 completed by a demo session focussed on the propagation phase contrast imaging procedures using monochromatic X-rays.

Speaker: Alberto Bravin (European Synchrotron Radiation Facility)

5:55 PM → 6:25 PM Unification of the ESRF tomographic processing software

The ESRF tomography acquisition and processing software has traditionally suffered from fragmentation across the different beamlines, resulting in many different solutions for similar problems.
The associated maintenance and development costs have severely hindered its progress.
We are currently re-thinking our acquisition and processing workflows from scratch, with a unified underlying solution across the board. The centralization of the development is expected to deliver a uniform and standardized experience on all the ESRF tomography beamlines, and to provide high quality software.
In this talk, we will explore the unified development strategy, and its most relevant software projects.

Speaker: Nicola Vigano' (European Synchrotron Radiation Facility)

6:25 PM → 6:50 PM Interactive Q&A (moderator: F. De Carlo)

Wednesday, February 24

3:00 PM → 3:05 PM Short introduction to Day 3

3:05 PM → 3:50 PM Work- and Dataflow for CT at BAMline

After a general presentation of the beamline, specifically the workflow for ex-situ CT at BAMline is presented. Although being used in a broad variety of research fields the usual workflow for CT experiments is in most cases similar in terms of sample mounting, tomographic scan and reconstruction. Specific scanning schemes allow for a preview reconstruction carried out during the scan. A detailed description of the used hardware as well as the self-coded programs applied in the data pipeline will be given. This will be accompanied by a practical demonstration of the software involved in the entire process.

Speaker: Henning Markötter and Michael Sintschuk (Helmholtz-Zentrum Berlin (BESSY II))

3:50 PM → 4:15 PM Interactive Q&A (moderator: L. Mancini)

4:15 PM → 4:30 PM Break

4:30 PM → 5:10 PM User interface at the P05 Nanotomography

Most users at the Nanotomography endstation at P05 are not very experienced in synchrotron tomography measurements, as they are coming from very different fields, e.g. Biologist, Geologist or Medics. The setup of a transmission x-ray microscope (TXM) however is often more complex with respect to sample alignment, different detector choices and varying scan parameters. An in-house developed control GUI (graphical user interface) has been set up at the instrument, allowing users to switch between different cameras, to choose different image settings (zoom, histogram etc.), to align the sample in the direct beam as well as in the TXM mode, and to start the scans with different parameters (e.g. exposure times, rotation speed…). The structure of the GUI is set up in such a way, that it is mainly self-explanatory and that all main features are covered in this one application. The structure in which it has been organized serves as an intuitive step by step guide, which reduces at the same time the risk of potential accidents drastically. In a separate Reconstruction GUI running on the DESY computer cluster, the users can start the reconstructions themselves, already right after the first scan is finished. In this way, it is possible for the user to check the reconstruction quality and adapt e.g. scan parameters or sample preparation methods.

Speaker: Silja Flenner (Helmholtz-Zentrum Geesthacht (DESY))

5:10 PM → 5:35 PM Interactive Q&A (moderator: A. Rack)

5:35 PM → 6:05 PM High-throughput 3D Imaging at KARA

Speaker: Tomas Farago (ANKA – KIT)

Abstract_KIT.pdf

6:05 PM → 6:30 PM Interactive Q&A (moderator: A. Rack)

Thursday, February 25

3:00 PM → 3:05 PM Short introduction to Day 4

3:05 PM → 4:10 PM MicroCT pipeline at the SYRMEP beamline of Elettra

Speaker: Amal Abouelhassan, Adriano Contillo, Francesco Brun and Lucia Mancini (Elettra Sincrotrone Trieste)

Abstract_Elettra.pdf

4:10 PM → 4:35 PM Interactive Q&A (moderator: C. Rau)

4:35 PM → 4:50 PM Break

4:50 PM → 5:30 PM Collecting and analyzing data at Beamline 8.3.2 (microCT) at the Advanced Light Source

I will demonstrate the process of setting up scans, collecting data, and doing image processing at Beamline 8.3.2 (microCT) at the Advanced Light Source (ALS) at Lawrence Berkeley National Laboratory. Like many of the beamlines at the Advanced Light Source (ALS), Beamline 8.3.2 uses Labview for beamline and enstation control, which provides convenient graphical interfaces for doing many tasks, and I will demonstrate how these work for users. I will also demonstrate the two approaches to data analysis we are using. One is based on workstations located at the beamline, and uses both python scripts and a graphical interface called Xi-CAM. The other is based on using NERSC, our local high performance computing center. This second approach uses high performance data transfer with globus and the computing jobs are launched through a jupyter web interface.

Speaker: Dilworth Y. Parkinson (Advanced Light Source)

5:30 PM → 5:55 PM Interactive Q&A (moderator: V. Nikitin)

5:55 PM → 6:25 PM Environment for full-field tomographic reconstructions at MAX IV beamlines

Speaker: Zdenek Matej (MAX IV)

Abstract_MAXIV.pdf

6:25 PM → 6:50 PM Interactive Q&A (moderator: V. Nikitin)

Friday, February 26

3:00 PM → 3:05 PM Short introduction to Day 5

3:05 PM → 4:05 PM Operation at the TOMCAT beamline: latest developments from acquisition to data visualisation

In this workshop, we will first give a short presentation (~20 min) on how full field tomography is performed in a standard way at TOMCAT. The latest developments achieved to ease the operation will be presented: hdf5 data handling, reconstruction pipeline optimisation, offline HPC cluster and data management.
In a second part, a live interactive demo and discussion round (~40 min) will be proposed focusing on the ultra-fast tomography end-station. Based on practical examples and requests of the audience, information will be given on the different triggering options, the adequate acquisition strategy and the large amount of data generated.

Speaker: Federica Marone and Christian Schlepuetz (Swiss Light Source)

4:05 PM → 4:30 PM Interactive Q&A (moderator: L. Mancini)

4:30 PM → 4:45 PM Break

4:45 PM → 5:45 PM Plenary discussion (moderator: F. De Carlo)

5:45 PM → 6:00 PM Wrap up, summary & farewell