EVENT SUMMARY - The QUANTIM Hackathon

The QUANTIM Hackathon, November 26-27 (organized by LINXS, contact: rajmund.mokso@maxiv.lu.se)

Special focus:

Cellular materials in biomedicine and materials science

Invited experts:

E. Ando, G. Lovric, Vedrana Dahl, Anders Dahl

Format:

- 24 hours challenge solving with experts in image analysis, biomedicine and materials
- local and external experts help user groups to find the right approach to quantify their tomographic images
- create environment for cross-fertilization between diverse groups but in need of similar image quantification tools.
- Initiation into the principles of image quantification, introducing tools and terminology.

Schedule:

Day 1: (12:00 – 18:00)

-       5 min intro into to the challenges by each participant
-       3x30 min tutorials by invited speakers
-       setting up data / software and defining strategies
-       start coding
-       summary of the day and how to continue

19:00- 21:00 DINNER: establishing networks for collaboration

Day 2:  (8:30-14:00)

-       coding / consulting experts
-       interpretation of results and identifying what did not work out
-       next steps

parallel program for invited experts:

-       invited + local organizers discuss concepts of common platforms / frameworks for collaboration on image quantification
-       prepare document with recommendations on how to facilitate image quantification collaborations (common frameworks / sharing scripts / short term visits)

Challenges to work on / participants:

-       Lung hypertension: Christian Norvik , Niccolo Peruzzi, (Karin Tran Lundmark) – Med LU
-       barley/wheat grain mutation: Nick Sirijovski, Mats Hansson – Bio LU
-       skin hydration and formulations,  Enamul Mojundar - Malmo
-       liver fibrosis, Anja Schmidt Christensen, LU and Malmo
-       maybe one project from CPH – to be confirmed

Next hackathons:
Porous media – fibers – unique samples  

Event summary

The 24 hours Quantim hackathon addressed six challenges: (i) Pulmonary vascular pathobiology, (ii) Liver tissue alterations caused by fibrosis, (iii) topical formultions applied to mammalian skin, (iv) trabecular bone architecture (v) Lybian desert glass microstructure and (vi) barley and oat seed segmentation. Each topic was brought by the scientists in charge of the interpretation of the relevant tomographic datasets obtained at one or multiple synchrotron / neutron facilities and the microtomograph at LTH. Between the 18 participants, we could welcome scientists from Lund and Copenhagen with the above mentioned scientific questions and datasets, complemented by the experts in image analysis from Lund, Copenhagen (QIM), France and Switzerland. Using the computing resources of LUNARC, 3D images for each scientific case were visualized and quantitative analysis was started. As the outcome of the hackathon, we established collaboration between scientist in the field of biology, geology with image analysis experts.