Attendees

• Zach, Eric, Elaine, Greg, TomG, Scooter, TomF

On-site Genentech Hall N436A

Agenda

• Elaine presents DICOM software review
• ChimeraX 1.4 release schedule
• NIAID contract
• Review Action Items listed below

Discussion Notes

• Computer security audit
  • Scooter had 10 half-hour meetings in past week, not much progress.
  • Scooter working on IS3 documentation on web site.
  • TomF concerned that expiring SSL certificates won't be renewed by UCSF IT if some security issues are not fixed such as Opal struts component.

• Demonstration of DICOM viewers by Elaine
  • Showed extensive ChimeraX DICOM written 2 years ago including example data sets.
  • Will show Slicer and Horos.
  • Both Slicer and Horos remember data sets you have opened in a database.
  • Showed lung CT scans from RIDER dataset with cancer tumor segmentations found by different segmentation algorithms.
  • Current Slicer is much different than 2019 version that Elaine used before.
  • Slicer does not correctly show Jason Rubenstein's 4D echocardiogram. Appears to show 1000 2d frames as 1000 time points instead of 25 time points with 40 slices per time.
  • Slicer shows 3 orthogonal views. Can also show volumetric 3D rendering.
  • Showed ChimeraX on same lung cancer segmentation data set.
  • Showed Horos which has the same problem as Slicer with Jason Rubenstein data.
  • Horos has hundreds of options for rendering and other preferences.
  • Significant weakness of ChimeraX with DICOM is it does not indicate modality (CT scan, MRI scan, segmentation, ...) unless that is in the name of the "study".

Action Items

• Move toolshed to it's own IP address and it's own Apache instance -- Greg/Scooter
• Set up toolshed test instance (UCSF only) -- Greg/Scooter
• Clean up VirtualHosts on our web servers -- Greg/Scooter
• Move webservices to https only and extensively test chimera to make sure it works
• Create self-signed certificate for webservices-test -- ongoing, Greg has run into a weird error
• Document new vpn setup on Linux -- Scooter
• Set up 2-factor authentication for hal2 vpn -- Scooter
• Audit followup -- Scooter