Tracks Widget — Viewing and Exporting Cell Lineages

What this widget does

The Tracks Widget visualises the temporal tracks produced by the omero-screen pipeline’s --track option (see Temporal Tracking). Once a live-cell plate has been tracked, every nucleus carries a stable track_id across time and a parent_track_id linking daughters to their mother at divisions. This widget overlays those tracks on the well image, lets you inspect a single lineage, export one track’s measurements for analysis, and hand a well off to Mastodon for manual curation.

It does not generate tracks — that happens in the pipeline. Here you view, export, and protect them.

Before you start

  • The plate must have been run with omero-screen <id> --stitch --track, and imported into CellView (cellview import-plate <id>), so the track_id columns exist.
  • Load the well first with the Welldata Widget — the Tracks Widget reads the well that is currently loaded in the viewer.

Opening the widget

In Napari, go to Plugins → Omero Screen Napari → Tracks Widget. The panel stacks several sections, each with its own button:

  1. Load tracks
  2. Export track CSV
  3. Export well for Mastodon
  4. Pin plate
  5. Unpin plate

If the lower buttons are cut off, drag the dock taller or undock it.

Load tracks

Fills in (or leave Well blank to use the currently-loaded well), then click Load tracks.

Field What to enter
Well Well position, e.g. B2. Blank = the loaded well.
Color by track_id (rainbow) or cell_cycle (if cell-cycle analysis ran).
Tail length How many past frames trail behind each track head (default 10).
Show divisions (lineage) Off by default. When on, the division lineage graph is passed to the Tracks layer so mother→daughter links are drawn. Building the graph for thousands of divisions can briefly freeze the UI, so it is opt-in.

A napari Tracks layer appears, overlaid on the nuclei. The track positions are scaled to match the image, so they sit directly on the cells. Scrub the time slider to watch tracks move; a division shows as one track splitting into two.

Note

If you see “No track data in the loaded plate”, the plate was not tracked or not yet imported into CellView. Re-run the pipeline with --track (and --stitch), then cellview import-plate.

Inspecting a single lineage (napari-arboretum)

For the lineage tree of a single track, use the napari-arboretum plugin (installed as a dependency), which is purpose-built for this:

  1. Open Plugins → arboretum → Arboretum.
  2. Select the tracks layer in the layer list.
  3. Double-click a track in the viewer — Arboretum draws that founder’s lineage tree, with divisions as branch points.

We delegate the tree view to Arboretum rather than reinventing it — it is made by the same lab that contributed napari’s Tracks layer.

Export track CSV

To pull one track’s full measurement time-course out for downstream analysis (e.g. picking the longest, cleanest tracks):

  1. Enter the track id (read it off the Tracks layer or the Arboretum tree).
  2. Optionally set the Well.
  3. Click Export track CSV and choose a save location.

The CSV contains every measurement column for that single track across time.

Export well for Mastodon (CTC)

Prepares a well for manual curation in Mastodon as a Cell Tracking Challenge bundle:

  1. Optionally set the Well.
  2. Click Export well for Mastodon (CTC).

This writes ~/mastodon_exports/plate_<id>_<well>_ctc/ containing per-frame mask*.tif label images (from the cached zarr — no image copy), res_track.txt (the lineage), manifest.json (for the CellView round-trip) and a README.txt with the exact CTC-import steps. Import it via Mastodon’s Import from CellTrackingChallenge — this preserves lineages and divisions, which the CSV importer does not. See the Live-cell tracking overview for the full walkthrough.

Note

Use the CTC importer, not Mastodon’s CSV importer: the CSV importer creates spots but no links, so it silently drops every track. The bundle is written on demand per well (not at cache-build time), since it includes a per-frame TIFF stack.

Pin / Unpin plate

The OME-Zarr cache is size-bounded and evicts least-recently-used plates. If you will curate a well in Mastodon over time (a separate Fiji session that can span days), protect it first:

  • Pin plate — exempt the loaded plate from eviction. The pin persists across napari restarts.
  • Unpin plate — release it when you are done curating, so it can be reclaimed. The button also reports which plates are still pinned.

Pinning is deliberately a manual choice: caching a plate does not mean you are curating it, and pinning everything would defeat the cache.