ThripsDetection

Lab tools for scoring chilli thrips injury on young blueberry plants from rover RGB photos (UF / IFAS, Gainesville).

The shipped job is a plant score, not an insect count. Insects are too small to see on these frames. Damage shows on the young flush: bronze or silver patches, cup, crinkle, curl.

• AGENTS.md — full handoff for another agent: setup, local vs GPU storage, exports, UI change map
• PLAN.md — locked method: how we tile, what we label, which models we will bake off, how a plant score is formed
• annotator/ — local labeling UI (tissue → injury → curl)
• segment_and_tile.py / filter_tube_tiles.py — Center BiRefNet plant crop, then 512 px tiles
• dino_probe.py, probe_plant_scores.py, compare_classical_scores.py, calibrate_thrips_scores.py — early probes
• human_thrips_scores.csv — whole-plant scores for the first 36 rover photos

Photos, foliage tiles, the SQLite label database, and GPU passwords stay off git. They live in annotator/data/ on the machine that runs the UI, or on the GPU server. The annotator clones this repo for the app, then uploads the tiled folder from the server. See ANNOTATOR.md.

The annotator runs on one computer. Clone this repo, then see ANNOTATOR.md.

python3 -m venv .venv
source .venv/bin/activate
pip install -r annotator/requirements.txt
python -m annotator --port 8765

Open http://127.0.0.1:8765.

1. Type your name. Continue a session, upload a tiled folder, or (if this computer has a local settings file) send raw photos to the GPU. Work stays in annotator/data/sessions/.
2. For each square: new growth / old leaves / not a leaf. Old leaves and not a leaf save as skip.
3. If new growth: healthy / injured / skip, then curl yes / no.
4. Mixed new growth = injured. Lime crinkle with no bronze or cup = healthy. No 1–5 on a square.
5. Keys: 1 2 3 tissue then injury, Y N curl, Z undo, Esc clears this tile.
6. Close and reopen: Home is the default. Continue to the last session, or pick one. Review the four columns, then export CSV.

This kit does not store a GPU password. Do not add annotator/data/settings.json.

• Score tiles 1–5
• Train attention-MIL or insect detectors
• Put GPU passwords, API keys, or raw rover photos in this repository