Live-cell tracking

OMERO-Screen can follow individual cells through time. On a live-cell timelapse, every segmented nucleus is linked across frames so that it keeps one track_id for its whole lifetime, and each division is recorded as a parent → daughter link. Tracks go into the same CellView database as every other measurement. You can explore them in napari, correct them by hand in Mastodon, and, on PIP-FUCCI plates, repair and review them with an edit log.

The workflow

omero-screen --stitch --track           1  generate tracks
     │  Trackastra links nuclei across frames; track_id / parent_track_id
     │  go into the measurements
     ▼
cellview import plate                   2  tracks land in CellView
     ▼
napari: Tracks widget                   3  view, inspect lineages, export
     ├──▶ Mastodon (Fiji)               4a manual curation of any plate
     └──▶ repair + review in napari     4b PIP-FUCCI plates: edit log

Step	Tool	Guide
1–2	omero-screen --stitch --track, cellview import plate	Generate tracks
3	Tracks widget	Tracks widget
4a	Mastodon	Curate in Mastodon
4b	cellview repair-tracks, Track Review widget, cellview curate	Repair and review

Raw and curated columns

Every tracked cell carries two pairs of columns:

• track_id_raw / parent_track_id_raw: the tracker’s output. Nothing ever changes them.
• track_id / parent_track_id: the current best lineage. Repair and curation write here.

Keeping the raw pair means every correction can be audited, and repeated, from the tracker’s original output.