diff --git a/meeting-notes.md b/meeting-notes.md index 0fb4104..f3c3e92 100644 --- a/meeting-notes.md +++ b/meeting-notes.md @@ -4,6 +4,118 @@ These are the public notes for the JuliaHealth Community. Notes are published publicly here and are available for comments and review on the [public HackMD](https://hackmd.io/@AQm1lp9PSPyir6IoTPAZeQ/SJNu_d3uh). Additionally, the notes are [hosted publicly on the GitHub](https://github.com/JuliaHealth/juliahealth.github.io/blob/dev/meeting-notes.md) and are open for PRs or edits as needed. +# October 27 2023 + +**In Attendance:** Jakub Mitura, Phil Vernes, Jay Sanjay + +**Location:** Virtual (JuliaHealth Google Meet) + +**Summary:** Jakub Mitura presented on his work for MedEval3D, discussion on medical imaging, debrief from the OHDSI Symposium, and some initial conversation about GSoC + +**Keywords:** #medical #imaging #gsoc #ohdsi + +## Agenda + +1. New member introductions +2. New contributor round-up! +3. Running tasks follow-ups: + * Short-term task follow-ups: + * Jacob shares info on waste water management + viral load information + * Long-term task follow-ups: + * Creating a template repository +4. Presentation by Jakub Mitura on sub-ecosystem he created for working with CT, PET, and other medical imaging types of data. +5. Debrief from OHDSI Symposium (Observational Health research venue) +6. Google Summer of Code Project Discussion + * JuliaHealth documentation improvement + * Observational Health Tooling improvements and discussion + * Visualization tools +7. Upcoming and ongoing research opportunities + * Call for collaboration on using JuliaHealth observational health tools for multi-site study +8. Medical Imaging Extension for Real World Evidence exploration +8. Open discussion + +## Meeting Outcomes + +### Short-Term Outcomes + + + +### Long-Term Outcomes + + + +## Notes + +- New member introductions + - Phil Vernes + 3. Works at JuliaHub + 4. Developing platform for running Julia jobs + 5. Many people at JuliaHub using tools within epi + 6. Can solve many problems in DSL + - Jay Sanjay + 8. Started contributing to the JuliaHealth ecosystem + 9. Looking forward to collaborating +- Running tasks follow-ups: + * Short-term task follow-ups: + * Jacob shares info on waste water management + viral load information + * Long-term task follow-ups: + * Creating a template repository + * We need to have a data structure to hold metadata (DICOM, NIFTI, etc.) + * JuliaNeuro + * HDF5 for long-term storage + * Would be great to see everyone using this + * To work on this to bring this together + * Multiple packages could have same +5. Presentation by Jakub Mitura on sub-ecosystem he created for working with CT, PET, and other medical imaging types of data. + 6. Created three packages + 7. Mainly talking about MedEye3D + 8. Segment data and iterate to see what is going on + 9. Wanted to create tools for everything around model creation + 10. Wanted to make a viewer that is well-suited for the Julia ecosystem + 11. Most medical viewers are quite "old" + 12. Not really dynamic + 13. Hard to show changes within run-time + 14. Easy to get big increase in Julia + 15. Usually something like 10x's faster + 16. We do not yet standardize way to load data + 17. Metadata is saved to HDF5 format + 18. Can introduce dynamic annotations + 19. Can have layers and switch on and switch layers + 20. Can annotate for saying where is the problem in the viewer + 21. Viewer can dynamically update + 22. Questions + 23. Tested some semi-automatic algorithms + 24. Do evaluate repeat + 25. Makes it faster for evaluation and reviewing of medical images + 26. Depends on OpenGL and NVIDIA drivers + 27. Working on Docker container that keeps + 28. What segmentation algorithm? Approach? + 29. Based on Gaussian probability distributions + 30. Some relaxation applied + 31. Based mainly on the units and different kinds + 32. Becoming more interested in transformers + 33. Implemented in JAX but want to bring it into Julia + 34. Segmentation for bladder cancer in image analysis + 35. Restarted work recently in Julia + 36. Would be useful for others? + 37. New segmentation for other ecosystem within Julia +9. Upcoming and ongoing research opportunities + * Call for collaboration on using JuliaHealth observational health tools for multi-site study +10. Medical Imaging Extension for Real World Evidence exploration + 11. Idea was to implement package for medical imaging + 12. Pillars + 13. Computing statistics across medical imaging + 14. Complete datasets for experimetnign + 15. Feature segmentation and scanning + 16. Align probabilistic model between different scans + 17. Become easier for physicians + 18. ML model for complex models for image segmentation + 19. Thing to consider -- need more robustness for image alignment? + 20. SOme transformations are relatively easier to repair + 21. Elastic deformations + 22. If we want +12. Open discussion + # September 29 2023 **In Attendance:** Tiem van der Deure, Scott Jones, dx/dt @@ -84,6 +196,90 @@ Additionally, the notes are [hosted publicly on the GitHub](https://github.com/J - Many healthcare systems put together monitoring systems - NHS (in UK) dismantled their monitoring systems +# September 29 2023 + +**In Attendance:** Tiem van der Deure, Scott Jones, dx/dt + +**Location:** Virtual (JuliaHealth Google Meet) + +**Summary:** Discussion on viral load found in wastewater, GSoD for this fall/GSoC for next summer, and upcoming research opportunities and events + +**Keywords:** #databases #wastewater #interfaces #gsoc #ohdsi + +## Agenda + +1. New member introductions + +2. Running tasks follow-ups: + + 1. Short-term task follow-ups: + + 2. Long-term task follow-ups: + + - Creating a template repository + +3. Upcoming research opportunities and events + + 1. Not too early to start thinking about GSoC + + 2. Julia and OHDSI Symposium + +4. Infectious Disease load for various sewage water data + +5. Open discussion + +## Meeting Outcomes + +### Short-Term Outcomes + +- Jacob shares info on waste water management + viral load information + +## Notes + +- Introductions + - Tiem van der Deure + - University of Copenhagen PhD + - Vector-borne Disease Modeling + - Epidemiological modeling and climate effects on health + - Rafael Schoueten + - Scott Jones + - Heavily involved in healthcare IT + - dx/dt + +- Google Summer of Code + - Recently discovered by the team + - Google Season of Docs + - Best for long-term maintenance + - Significant challenge organizing in Julia docs ecosystem + +- OHDSI + Julia + - Working with EHR from EPIC is demanding + - Labour intensive albeit improving + - Turing modeling "making them work" + - Getting them to run + - Making it run fast enough + - Trade off ease-of-use for computation speed + - Requires significant mathematical ability for speed gains + +- Sewage water information for disease population estimations + - Weekly excerpt + - Infectious disease doctor + - Would be really neat to make some kind of app to check wastewater + - Propensity of viruses in ER + - Physician testing for rough understanding of what is happening in community + - Ability to look for multiple co-factors instead of just one disease + - Many healthcare systems put together monitoring systems + - NHS (in UK) dismantled their monitoring systems + +- Databases and JuliaHealth + - Show how to do the basics + - Common database errors + - How to address them + - Consider having more people working in this space? + - Not really a problem within ecosystem + - Look at drivers across all packages to see how things work in Julia ecosystem + - See how we can address issues across ecosystem + # August 25 2023 **In Attendance:** Edmund Miller, Jonathan Starr, Clark Evans, Kirill Simonov, Jacob Zelko @@ -177,7 +373,7 @@ Additionally, the notes are [hosted publicly on the GitHub](https://github.com/J - Coming from JuliaCon - Excited about Health stuff -- Interoperability of Julia with health research ecosystems (R ) +- Interoperability of Julia with health research ecosystems (R) - Easiest way to interoperate is to call them directly from the command line - Build your own executables - Most reliable/easiest