cellview review-queue

Sample cells per well and write a review queue for the Track Review widget.

cellview review-queue [OPTIONS] ID

Cells present at --start are followed to --stop on the curated lineage (automatic repair plus --log). A fixed-seed random sample per well is drawn; flagged cells and an --audit fraction of unflagged ones are queued.

Full --help output

Usage: cellview review-queue [OPTIONS] ID

  Sample cells per well and write a review queue for the Track Review widget.

  Cells present at --start are followed to --stop on the curated lineage
  (automatic repair plus --log). A fixed-seed random sample per well is drawn;
  flagged cells and an --audit fraction of unflagged ones are queued.

Options:
  --well TEXT                    Well to sample (repeatable).  [required]
  --start INTEGER                Frame at which cells are sampled.  [default:
                                 72]
  --stop INTEGER                 Last frame cells are followed to.  [default:
                                 168]
  --sample INTEGER RANGE         Cells per well.  [default: 50; x>=1]
  --audit FLOAT RANGE            Fraction of unflagged sampled cells queued as
                                 a random check.  [default: 0.2; 0<=x<=1]
  --seed INTEGER                 [default: 0]
  --mode [human|agent]           human: the agent proposes and the reviewer
                                 confirms. agent: the agent edits and decides
                                 alone (use a separate --out to compare runs).
                                 [default: human]
  --stationary-warn FLOAT RANGE  Warn when this fraction of a well's start
                                 cells is stationary yet expresses a reporter.
                                 [default: 0.05; 0<=x<=1]
  --log FILE                     Edit log to replay before following cells.
  --marker TEXT                  [default: Geminin]
  --out DIRECTORY                Directory for queue.json and sample.csv.
                                 [required]
  --help                         Show this message and exit.

Arguments

ID: INTEGER

Required.

Options

--well: TEXT

Required. Well to sample (repeatable).

--start: INTEGER = 72

Frame at which cells are sampled.

--stop: INTEGER = 168

Last frame cells are followed to.

--sample: INTEGER RANGE = 50

Cells per well.

--audit: FLOAT RANGE = 0.2

Fraction of unflagged sampled cells queued as a random check.

--seed: INTEGER = 0

 

--mode: CHOICE = human

human: the agent proposes and the reviewer confirms. agent: the agent edits and decides alone (use a separate --out to compare runs).

--stationary-warn: FLOAT RANGE = 0.05

Warn when this fraction of a well’s start cells is stationary yet expresses a reporter.

--log: FILE

Edit log to replay before following cells.

--marker: TEXT = Geminin

 

--out: DIRECTORY

Required. Directory for queue.json and sample.csv.