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Refactored some of the layout
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HackMD committed Nov 14, 2023
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### Short-Term Outcomes


- Jacob intro's Phil and Jakub
- Jacob follows-up with Phil

### Long-Term Outcomes


- Create a template repository for JuliaHealth

## 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
- Phil Vernes
- Works at JuliaHub
- Developing platform for running Julia jobs
- Many people at JuliaHub using tools within epi
- Can solve many problems in DSL
- Jay Sanjay
- Started contributing to the JuliaHealth ecosystem
- 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
- 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
- Presentation by Jakub Mitura on sub-ecosystem he created for working with CT, PET, and other medical imaging types of data.
- Created three packages
- Mainly talking about MedEye3D
- Segment data and iterate to see what is going on
- Wanted to create tools for everything around model creation
- Wanted to make a viewer that is well-suited for the Julia ecosystem
- Most medical viewers are quite "old"
- Not really dynamic
- Hard to show changes within run-time
- Easy to get big increase in Julia
- Usually something like 10x's faster
- We do not yet standardize way to load data
- Metadata is saved to HDF5 format
- Can introduce dynamic annotations
- Can have layers and switch on and switch layers
- Can annotate for saying where is the problem in the viewer
- Viewer can dynamically update
- Questions
- Tested some semi-automatic algorithms
- Do evaluate repeat
- Makes it faster for evaluation and reviewing of medical images
- Depends on OpenGL and NVIDIA drivers
- Working on Docker container that keeps
- What segmentation algorithm? Approach?
- Based on Gaussian probability distributions
- Some relaxation applied
- Based mainly on the units and different kinds
- Becoming more interested in transformers
- Implemented in JAX but want to bring it into Julia
- Segmentation for bladder cancer in image analysis
- Restarted work recently in Julia
- Would be useful for others?
- New segmentation for other ecosystem within Julia
- Upcoming and ongoing research opportunities
- Call for collaboration on using JuliaHealth observational health tools for multi-site study
- Medical Imaging Extension for Real World Evidence exploration
- Idea was to implement package for medical imaging
- Pillars
- Computing statistics across medical imaging
- Complete datasets for experimenting
- Feature segmentation and scanning
- Align probabilistic model between different scans
- Become easier for physicians
- ML model for complex models for image segmentation
- Thing to consider -- need more robustness for image alignment?
- Some transformations are relatively easier to repair
- Elastic deformations

# September 29 2023

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