3D histology with synchrotron micro-tomography: Symposium and hackathon– IPDD theme

• 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.

Register here

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

13:10-13:40 Andrew Cook (University College London) "Deep-phenotyping in the human fetal heart using synchrotron x-ray imaging"

13:40-14:10 Goran Lovric (Paul Scherrer Institute) “Deep learning based X-ray virtual histology"

14:10-14:30 Coffee break

14:30-14:50 Sophie Sanchez (Uppsala University)

14:50-15:10 Rajmund Mokso (Danish Technical University)

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 Data analysis at the QIM centre. 

16:40-17:00 Presentation of HALRIC project funding and CIPA data analysis network.

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 [dot] bech [at] med [dot] lu [dot] se (martin[dot]bech[at]med[dot]lu[dot]se)

Please contact josefin [dot] martell [at] linxs [dot] lu [dot] se (josefin[dot]martell[at]linxs[dot]lu[dot]se) for any practical questions.