Collaborative Computational Project in Synergistic Reconstruction for Biomedical Imaging

Second hackathon on algorithms benchmarking for tomographic reconstruction.

Monday, April 4, 2022 - 12:00 to Thursday, April 7, 2022 - 16:00

Venue: room MR13 of Centre for Mathematical Sciences in Cambridge.

The goal of the hackathon is to establish a framework for benchmarking numerous state-of-the-art iterative algorithms for CT and PET reconstruction, with a focus on randomized subset algorithms. In the previous hackathon, we have focused on implementing the selected algorithms in CIL (eg SGD, SAGA, SVRG, SPDHG, and accelerated methods) and have tested them on a toy 2D CT example. In this hackathon, we will seek to make the next step for evaluating the implemented stochastic optimization algorithms on large-scale CT and PET 3D reconstructions and real datasets.

Specific goals are:
• Agree on a suitable evaluation strategy, including metrics for image quality and algorithm performance (run-time, memory etc), taking into account parameter selection for algorithms
• Agree on suitable data sets for evaluation
• Implement quality metrics (e.g. based on tools from scikit-rt)
• Implement a framework to organize the data and the experiments, for example with Hydra
• Initial implementation of evaluation framework on a cluster (STFC or even distributed)
• Investigate feasibility of scope of evaluation

The organizers: Junqi Tang (local organizer), Claire Delplancke, Matthias J. Ehrhardt, Ashley Gillman, Zeljko Kereta, Evangelos Papoutsellis, Edoardo Pasca, Imraj Singh, Kris Thielemans


Monday 4
12:00-13:30 Lunch
13:30-14:00 Opening (hybrid)
14:00-14:45 Discussion about PET quality metrics (hybrid) Presentations: Robbie Twyman (15 min), Georg Schramm (5 min)
14:45-15:30 Discussion about CT quality metrics (hybrid)
15:30-16:00 Coffee break
16:00-17:00 Recap of discussion ; what needs to be implemented ? (hybrid)
17:00-18:00 organization of following days

Tuesday 5 - Wednesday 6
9:30 Brief progress report
9:40 Group work
11:00 Coffee break
11:30 Group work
12:30 Lunch
13:30-14:30 Progress report (hybrid)
14:30 Group work
15:30 Coffee break
16:00 - 18:00 Group work

Thursday 7
9:30 Brief progress report
9:40 Group work
11:00 Coffee break
11:30 Group work
12:30 Lunch
13:30-15:30 Conclusions and planning (hybrid)
15:30 Coffee break
16:00 End of event