cellview repair-tracks

Repair the tracked lineages of plate ID from segmentation flicker.

cellview repair-tracks [OPTIONS] ID

Reads the tracker’s immutable track_id_raw / parent_track_id_raw and writes the curated track_id / parent_track_id, so re-running gives the same result. Only plates with a mitotic marker (geminin) are repaired.

Full --help output

Usage: cellview repair-tracks [OPTIONS] ID

  Repair the tracked lineages of plate ID from segmentation flicker.

  Reads the tracker's immutable track_id_raw / parent_track_id_raw and writes
  the curated track_id / parent_track_id, so re-running gives the same result.
  Only plates with a mitotic marker (geminin) are repaired.

Options:
  --well TEXT    Restrict to this well (repeatable). Default: every well.
  --marker TEXT  Channel whose nuclear signal is degraded at anaphase (PIP-
                 FUCCI: geminin).  [default: Geminin]
  --dry-run      Report what would change; write nothing.
  --events FILE  Write every repair decision (rule, frame, position) to this
                 CSV.
  --help         Show this message and exit.

Arguments

ID: INTEGER

Required.

Options

--well: TEXT

Restrict to this well (repeatable). Default: every well.

--marker: TEXT = Geminin

Channel whose nuclear signal is degraded at anaphase (PIP-FUCCI: geminin).

--dry-run

Report what would change; write nothing.

--events: FILE

Write every repair decision (rule, frame, position) to this CSV.