Curate in Mastodon

Automatic tracking is never perfect, so tracks are corrected by hand in Mastodon, a Fiji tool for editing tracks. The image comes straight from the local OME-Zarr cache; the tracks come from a Cell Tracking Challenge (CTC) bundle exported by the Tracks widget.

Important

Use the CTC importer, not the CSV importer. Mastodon’s CSV importer creates spots but no links, so it silently drops every track and lineage. Its label-image importer cannot create division links. Only the Cell Tracking Challenge importer rebuilds full lineages, divisions included, because it reads the parent of each track from res_track.txt.

1. Export the bundle

Cache the plate and open the well in napari, then click Export well for Mastodon (CTC) in the Tracks widget. It writes ~/mastodon_exports/plate_<id>_<well>_ctc/ containing:

  • mask000.tif … mask<T-1>.tif: one nucleus label image per frame, read from the cache. Each cell’s pixel value is its CTC track label.
  • res_track.txt: the lineage table, one line L B E P per track (label, first frame, last frame, parent label; 0 for a founder). Labels are renumbered 1..N in order of first frame, matching the masks.
  • manifest.json: maps each CTC label back to its CellView track_id, with per-frame centroids. Keep it and don’t edit it.
  • README.txt: these import steps with your paths filled in.

Before a long curation session, Pin the plate in the Tracks widget so the cache does not evict it, and Unpin it afterwards.

2. Open the image

In Fiji:

  1. Plugins → Tracking → Mastodon → new from OME-NGFF…

  2. Paste the path to the well’s image group, the multiscale 0 group inside the plate store:

    ~/omero-cache/zarr/plate_<id>.zarr/<row>/<col>/0

    for example ~/omero-cache/zarr/plate_4155.zarr/B/2/0. Don’t point at the plate root or the well folder.

  3. Click Detect datasets, select the listed row, click OK, and save the BDV XML when asked.

  4. The image opens in BigDataViewer. P opens the side panel for per-channel contrast, 1 and 2 switch channels, and F toggles a fused overlay.

3. Import the tracks

In the main Mastodon window choose File → Import → Import from CellTrackingChallenge. Select the bundle folder and set the file pattern to mask%03d.tif (three digits, starting at 0). Mastodon reads the parent and division links from res_track.txt.

4. Curate

Click the same group-lock number (e.g. 1) in both the BigDataViewer and TrackScheme windows; double-clicking a spot then moves both views to it. Save your work as a .mastodon project outside the cache, so it survives the plate being evicted.

Bringing corrections back (planned)

Export the corrected tracks with File → Export → CellTrackingChallenge. Writing them back into CellView is not implemented yet. The plan is to map each corrected spot onto its CellView row by per-frame centroid, using manifest.json as the anchor, and write the result to track_id / parent_track_id, leaving the _raw columns as the audit trail.

Until then, the corrected CTC export (kept with its manifest.json) and the .mastodon project are the record of your corrections. On PIP-FUCCI plates, the napari review workflow already writes corrections back.