NTT DATA UCSF NIAID SEB Subcontract 2021 Task Order #2

March 1, 2021 - February 28, 2022 from ​Google Doc

1. General ChimeraX improvements to support NIAID (Eric: 20%)

2. Support the NIH 3D pipeline development, including any changes to ChimeraX to support ongoing development. (Eric: 15%)

3. Improve multi-person VR (Tom: 35%)
   1. Create video tutorials in how to use multi-person VR
   2. Hold VR office hours to train researchers to use VR capabilities
   3. Allow participants to add models from local files during a VR session
   4. Set up VR meeting servers for Africa, Europe, Asia

4. Human Biomolecular Atlas Program (HuBMAP) multiscale visualization (Eric: 30%)
   1. Develop ChimeraX tool to browse and select HuBMAP datasets for loading

5. Enhance ChimeraX’s segmentation capabilities
   1. Investigate increased use of simple ITK to support segmentation (Tom: 15%)
   2. Investigate utilizing web services to support more complex machine learning-based segmentation algorithms (Tom: 15%)
   3. Investigate reading and displaying segmentation format(s) available from imaging databases (tissue microscopy, cancer imaging data, etc.) (Tom: 10%)

6. DICOM (Tom: 25%, Eric: 5%)
   1. Improve ability to visualize and analyze medical images in VR with ChimeraX
   2. Develop browser-style interface to show DICOM dataset contents and associated metadata such as sample characteristics

7. Outreach
   1. Instructional material and tools documentation. (20%)
      1. Detailed instructions for all features shall be provided in a user manual
      2. Written user guides and tutorials shall be available as an HTML page

8. Administration (10%)
   1. Submit monthly written reports of accomplishments