Overview

celltraj contains the trajectory-analysis layer for live-cell imaging data. The current modules cover:

• image and mask preprocessing,

• per-cell feature extraction,

• HDF5-backed trajectory objects,

• trajectory embedding and state decomposition,

• Markov/Koopman-style dynamical modeling,

• spatial and boundary-aware feature utilities, and

• translation between morphodynamic states and molecular measurements.

The package predates sitelab, so some APIs still reflect notebook-era research workflows. Current modernization work is focused on making these APIs cleaner, package-relative, testable, and easier for sitelab to call.