# Repair and review (PIP-FUCCI)

On plates with a geminin channel (PIP-FUCCI), tracks can be repaired automatically and then checked by a reviewer in napari, with an agent's help if you like. Nothing edits the tracker's output. Corrections are entries in an **edit log**, and the curated lineage is always rebuilt from the automatic repair plus that log, so it can be reproduced, inspected and undone.


# 1. Automatic repair

Cellpose often splits one nucleus into pieces, and the tracker then reports divisions that never happened. The repair accepts a division only when both daughters lose geminin, which is degraded at anaphase. It merges touching pieces back, detaches mislinked neighbours and rejoins tracks that restart.

``` bash
uv run cellview repair-tracks 5054 --dry-run     # report only
uv run cellview repair-tracks 5054               # write track_id / parent_track_id
```

The repair reads `track_id_raw` / `parent_track_id_raw` and writes `track_id` / `parent_track_id`, so running it again gives the same result. `--well` restricts it to some wells, `--marker` names the mitotic marker channel (default `Geminin`), and `--events FILE` writes every repair decision to a CSV.


# 2. Review queue

Cells present at a start frame are followed to a stop frame. A random sample is drawn per well. The cells the walker flags (lost, gaps, fragments, phases out of order, rare outcomes) are queued, plus an audit fraction of the unflagged ones:

``` bash
uv run cellview review-queue 5054 --well C2 --well C3 --sample 50 \
    --start 72 --stop 168 --audit 0.2 --seed 1 --out review/
```

This writes `review/queue.json` and `review/sample.csv`. Pass `--log review/edits.jsonl` to build a queue on top of corrections already made.


# 3. Filmstrips

A filmstrip crops a window that follows the cell through every frame, with its PIP, geminin and area traces underneath:

``` bash
uv run omero-screen-images --env production track 5054 C2-t72-L524
uv run omero-screen-images --env production track 5054 \
    --queue review/queue.json --log review/edits.jsonl
```


# 4. Track Review widget

Open **Plugins → Track Review Widget** and load `review/queue.json`. For each cell you can:

- link it to its continuation (click it, or press Shift-1…9 for a numbered candidate);
- unlink it, or add or remove a nucleus;
- split a nucleus, or draw one that was missed;
- mark mitosis, death or slippage, or exclude the cell;
- give a verdict.

*Next break* jumps along the track to the next problem and *Follow cell* keeps the cell centred. Edits go to `review/edits.jsonl` and verdicts to `review/decisions.json`.


# Working with an agent

With [napari-mcp](https://github.com/HocheggerLab/napari-mcp/tree/plugin-tools) installed, omero-screen-napari adds review tools to the agent through napari-mcp's plugin hook. The agent can go to a cell, show its filmstrip, rank candidate continuations and propose an edit. A proposal appears in the widget and is applied only when the reviewer confirms it.

``` bash
uv run --with "napari-mcp @ git+https://github.com/HocheggerLab/napari-mcp@plugin-tools" napari
claude mcp add --transport http napari http://127.0.0.1:9999/mcp
```

The plugin hook is on the `plugin-tools` branch of the HocheggerLab fork until upstream napari-mcp releases it.


# The edit log on the command line

``` bash
uv run cellview curate show review/edits.jsonl
uv run cellview curate add review/edits.jsonl link \
    --plate 5054 --well C2 --cell 72:524 --frame 156 --label 3132
uv run cellview curate undo review/edits.jsonl --plate 5054 --well C2
uv run cellview curate replay review/edits.jsonl --plate 5054 --write
```

`add` validates an edit against the plate before appending it. `undo` appends a revert entry instead of deleting anything. `replay` rebuilds the curated lineage from the automatic repair plus every live edit; `--write` stores it in CellView. Every edit type and option is in the [CellView CLI reference](../cellview/reference/cli/index.md).