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