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Expand Up @@ -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
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- 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
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- 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
Expand Down

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