NTT_DATA_UCSF_NIAID-SEB_Subcontract_2021 Task Order #2

March 1, 2021 - February 28, 2022

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%)

• Create video tutorials in how to use multi-person VR
• Hold VR office hours to train researchers to use VR capabilities
• Allow participants to add models from local files during a VR session
• Set up VR meeting servers for Africa, Europe, Asia

4. Human Biomolecular Atlas Program (HuBMAP) multiscale visualization (Eric: 30%)

• Develop ChimeraX tool to browse and select HuBMAP datasets for loading

5. Enhance ChimeraX’s segmentation capabilities

• Investigate increased use of simple ITK to support segmentation (Tom: 15%)
• Investigate utilizing web services to support more complex machine learning-based segmentation algorithms (Tom: 15%)
• 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%)

• Improve ability to visualize and analyze medical images in VR with ChimeraX
• Develop browser-style interface to show DICOM dataset contents and associated metadata such as sample characteristics

7. Outreach

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

8. Administration (10%)

• Submit monthly written reports of accomplishments