  The processing and analysis of computed tomography (CT) imaging is important
for both basic scientific development and clinical applications. In AutoCT, we
provide a comprehensive pipeline that integrates an end-to-end automatic
preprocessing, registration, segmentation, and quantitative analysis of 3D CT
scans. The engineered pipeline enables atlas-based CT segmentation and
quantification leveraging diffeomorphic transformations through efficient
forward and inverse mappings. The extracted localized features from the
deformation field allow for downstream statistical learning that may facilitate
medical diagnostics. On a lightweight and portable software platform, AutoCT
provides a new toolkit for the CT imaging community to underpin the deployment
of artificial intelligence-driven applications.
