cellular-imaging-amsterdam-umc/cisegmentation
Agent skills for the Bilayers CI Segmentation workflow and its measurement databases.
Inspect and query CI Segmentation geometry companion databases in DuckDB or SQLite, including final-mask WKB polygons, holes, disconnected components, per-Z outlines, native Spotiflow subpixel points, calibrated transforms, bounding-box filtering and safe links to measurement objects.
Analyze CI Segmentation DuckDB or SQLite databases for morphology, intensity, mask relationships, spot assignments, spatial neighbors and contacts, Pearson/Manders colocalization, trajectories, cell/nucleus divisions, and linked WKB polygons or subpixel spot points; includes SQL, pandas, calibration and interpretation.
Configure, launch, monitor, and recover the Bilayers CI Segmentation workflow for OME-Zarr images or HCS plates using Cellpose, Cellpose-SAM, StarDist, InstanSeg, or Spotiflow, including spot-only detection, spatial and colocalization measurements, cell/nucleus lineages, independent spot trajectories, and separate geometry databases.