Welcome to 3D histology with synchrotron micro-tomography: Symposium and hackathon!
When: 6–7 December 2023.
Symposium at MAX IV 6 December: 12:00–17:00
Hackathon at LINXS 7 December: 9:00–14:00
Please indicate in the registration if you will attend both days or not.
Where: MAX IV, large conference room “MAX III”, Fotongatan 2 (6 Dec) and LINXS (7 Dec).
Who can benefit: All researchers in the fields of Medicine, Biology and Soft Materials, who are interested in 3D imaging methods, virtual histology, or just curious about synchrotron based micro-tomography are welcome to sign up.
Description
Applications of advanced x-ray micro-tomography to complement standard microscopy techniques. With volumetric imaging of soft tissue samples, virtual slicing and 3D visualization bring histological studies to the next level. This event is a combination of symposium on Wednesday afternoon with presentation and discussions of possible applications, followed by a hackathon on Thursday morning where users who have already collected data can work with our data analysis experts on segmentation and data extraction.
The workshop is organised by the working group Biomedical Imaging within the IPDD theme, and has a limit of 40 participants, so don’t wait to register!
Invited speakers: Andrew Cook from UCL in London and Goran Lovric from Swiss Light Source, PSI
Preliminary Programme
December 6
Location: MAX IV, large conference room “MAX III”, Fotongatan 2.
12:00-13:00 Lunch at MAX IV
13:00-13:10 Welcome by MAX IV director Marjolein Thunnisen
13:10-13:20 Introduction by Martin Bech
13:20-13:50 Goran Lovric (Paul Scherrer Institute) “Deep learning based X-ray virtual histology"
13:50-14:00 Carl Troein (CIPA, Lund University), "User support with image processing and analysis via CIPA at Lund University"
14:00-14:30 Coffee break
14:30-14:50 Sophie Sanchez (Uppsala University) “Three-dimensional virtual bone histology: a new insight into vertebrate skeletal evolution”
14:50-15:10 Anders Bjorholm Dahl (Technical University of Denmark), “Data analysis at the QIM centre”
15:10-16:00 Tour of MAX IV experimental hall
16:00-17:00 Future opportunities:
16:00-16:20 Elisabet Englund, Karin Tran Lundmark and Martin Bech (Lund University), ”From idea to image analysis”
16:20-16:40 Andrew Cook (University College London) "Deep-phenotyping in the human fetal heart using synchrotron x-ray imaging"
16:40-16:50 Jakob Dissing Øster (Rigshospitalet, Denmark and HALRIC ambassador), “Applying for HALRIC pilot projects”
December 7
Location: LINXS
9:00 - 14:00 Hackathon on segmentation and data extraction.
Hackathon theme: “AI based segmentation"
Invited experts: Jon Sporring (KU), Anders Bjorholm Dahl (DTU), Goran Lovric (PSI), Alexandros Sopasakis (LU), Sifra Bijl (UU)
9:00-9:15 Welcome
9:15-9:35 Presentation 1, Sifra Bijl
9:35-9:55 Presentation 2, Alexandros Sopasakis
9:55-10:15 Presentation 3, Jon Sporring
10:15-10:30 Break
10:30-12:00 Individual work with expert supervision
12:00-12:45 Lunch
12:45-13:45 Individual work with expert supervision
13:45-14:00 Conclusion of hackathon.
Organisers
The event is organised in collaboration with MAX IV.
For questions about the event, please contact Martin Bech martin.bech@med.lu.se
Please contact josefin.martell@linxs.lu.se for any practical questions.
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