High-resolution 3D microscopy is performed routinely at synchrotron radiation facilities in Europe, with applications in a range of bio-medical research proplems. In this workshop, expert synchrotron users and staff will present state-of-the-art case studies and we will discuss future possibilities both at MAX IV and abroad.

Participants will be welcomed to the workshop by Lund University Vice-Chancellor Erik Renström.

See the lineup of speakers below – more to be confirmed!

Title: Workshop: 3D biomedical imaging with synchrotron radiation: State-of-the-art and future possibilities

When: 30 May, 2024

Venue: Utblicken (room E 16), top floor Forum Medicum, Sölvegatan, Lund University, Sweden, or online via Zoom. A Zoom-link will be sent to all digital participants in time for the event.

Registration info: Please note that there is a limited number of available spaces for physical participants, and the registration for in-person participation will close when the venue is full! We also advise all participants to book accommodation as soon as possible, since this is generally a busy week in Lund.

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Confirmed Speakers

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Other info

Participation fee:

• 600 SEK for physical participation incl 3-course dinner at Kulturen's restaurant 

• 400 SEK for physical participation without dinner

• 200 SEK for online participation (via Zoom) 

• Program

  The program may still be subject to some change

  30 May

  Morning 10:00–11:00 Guided tour at MAX IV for registered participants

  11:30–12:30 Lunch and registration, Venue: E16 “Utblicken”, top floor of Forum Medicum, Sölvegatan, Lund

  12:30–12:40 Welcome by Vice-Chancellor Erik Renström

  13:00–13:10 Welcome and introduction, Martin Bech (LINXS/HALRIC) and Karin Tran Lundmark (LU)

  Session 1 Chairs: Kristina Djinovic Carugo (EMBL) and Rajmund Mokso (DTU)

  13:10–13:25 “3D virtual histology with synchrotron and advanced laboratory radiation: a new tool for clinical research and pathology”, Tim Salditt, Universität Göttingen, Germany

  13:25–13:40 “Hard X-ray nano-imaging of Toxoplasma gondii in different development stages”, Matthew Bowler, EMBL, France

  13:40–13:55 “Multimodal microscopy of atherosclerotic plaques to prevent strokes and heart attacks“, Isabel Gonçalves, Lund University, Sweden

  13:55–14:10 “Imaging lung function with synchrotron radiation“, Sam Bayat, Grenobles Alpes University, France

  14:10–14:25 Leg stretcher

  Session 2 Chairs: Marco Stampanoni (PSI) and Niccolo Peruzzi (LU)

  14:25–14:40 “Multiscale and multimodal imaging of bone”, Henrik Birkedal, Aarhus University, Denmark

  14:40–14:55 “Dynamic synchrotron-based X-ray microtomography to visualize the movement of human middle ear”, Anne Bonnin, Paul Scherrer Institut, Switzerland

  14:55–15:10 "3D imaging of pulmonary vascular disease", Karin Tran-Lundmark, Lund University, Sweden

  15:10–15:25 “Facilitating rapid and smooth data processing of Terabyte-scaled tomographic data”, Goran Lovric, Paul Scherrer Institut, Switzerland

  15:25–15:30 Exciscope flash presentation

  15:30–16:00 Coffee break

  Session 3 Chairs: Marjolein Thunnisen (MAX IV) and Trevor Forsyth (LINXS)

  16:00–16:15 “Virtual histotomography - a new tool for clinical cancer diagnostics”, Maximilian Ackermann, Johannes Gutenberg University Mainz, Germany

  16:15–16:30 “Investigation of cardiomyopathy using X-PCI (deep geno-phenotype of heart muscle disease)”, Kan Yan Chloe Li, University College London, UK

  16:30–16:45 “X-ray microscopy to explore life across scales“, Alexandra Pacureanu, ESRF

  16:45–17:30 Panel discussion and wrap-up session

  19:00– Optional dinner at Restaurant Kulturen in Lund

• Organisers

  Martin Bech (Lund University), Kristina Djinovic (EMBL Grenoble), Trevor Forsyth (LINXS, Sweden), Michael Krisch (ESRF, France), Niccolò Peruzzi (Lund University), Marco Stampanoni (PSI, Switzerland), Marjolein Thunnisen (MAX IV, Sweden), Karin Tran Lundmark (Lund University)

• Speaker abstracts

  Facilitating rapid and smooth data processing of Terabyte-scaled tomographic data 

  Goran Lovric, Paul Scherrer Institut, Switzerland

  The gradual shift to 4th-generation synchrotron sources has been boosting data production rates that nowadays easily reach orders of 1-10 TB of produced raw image data per day. This has not only created a big data bottleneck in terms of data storage, management, processing, and visualization, but also requires a revised approach in utilizing state-of-the-art data processing techniques. 

  In the present talk, I will describe our general concept of data flow in typical tomographic imaging experiments, enabling non-expert users to acquire, process and analyse data according to their needs. I will discuss the feasibility of tomography scans with processing times of several seconds up to a minute, for volumes of several hundreds of GBs and how we leverage recent developments in IT architectural frameworks to improve the overall user experience.

  3D virtual histology with synchrotron and advanced laboratory radiation: a new tool for clinical research and pathology

  Tim Salditt, Institut für Röntgenphysik, Universität Göttingen, Germany

  In order to unravel physiological and pathological mechanisms at the cellular level, structure and processes have to be visualized on a wide range of scales. Imaging at cellular and sub-cellular resolution is the realm of histology. For this purpose, the tissue obtained by surgical intervention or from a post mortem autopsy is cut into thin sections, stained and observed in an optical microscope. In conventional histology, images are obtained only of two-dimensional sections but not of the entire three-dimensional (3D) volume. In order to visualise and to quantify the cytoarchitecture in 3D, even deep in the tissue or organ, we use phase-contrast X-ray computerized tomography , as a tool for quantitative and fully digital 3D virtual histology. We have implemented the method using optimized phase retrieval, both at highly coherent synchrotron and at inhouse micro-focus sources. In a multi-scale approach, we combine parallel and cone beam illumination to cover a wide range of scales. Since the workflow is non-destructive and fully compatible with standard clinical pathology, we can perform correlative histology studies.

  In this talk we discuss image formation and advanced phase retrieval of propagation and inline holography data, the respective resolution limits, object constraints, scaling properties, as well as morphometric image analysis. We show how solutions and algorithms of mathematics of inverse problems and machine learning help us to meet the challenges of phase retrieval, tomographic reconstruction, segmentation, and more generally exploitation of bulky image data. All to the benefit of ambitious imaging projects such as mapping the human brain of fighting infectious diseases.

Contact:

For practical questions about the workshop, please contact josefin.martell@linxs.lu.se

The workshop is organised in the context of the LINXS IPDD theme.

KindLy supported by:

Hanseatic Life Science Research Infrastructure Consortium (www.halric.eu)

Sponsors:

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