---
license: mit
tags:
  - biology
  - plant-biology
  - microscopy
  - image-segmentation
  - cell-type-classification
  - cellpose
  - dinov2
  - lightgbm
library_name: rootscope
pipeline_tag: image-classification
---

# RootScope: Cross-species Root Cell-Type Classification from Confocal Microscopy Images

Trained weights for [RootScope](https://github.com/ct-tranchau/Rootscope).
Give RootScope a confocal cross-section TIFF of a root. It segments every cell
with Cellpose-SAM and labels each one as one of nine cell types: root cap,
epidermis, exodermis, cortex, endodermis, pericycle, stele, xylem, phloem.
The package downloads these weights on first use.

## Files

| File | Size | What it is |
|---|---|---|
| `v4/backbone.pt` | 346 MB | DINOv2 ViT-B/14, fine-tuned on cell crops (`meta.json` next to it records the architecture; keep them together) |
| `v4/lgbm_s42.joblib` | 170 MB | LightGBM, seed 42: one model per refinement round, scaler, feature names, class order |
| `v4/lgbm_s1.joblib`, `v4/lgbm_s7.joblib` | 170 MB each | the other two seeds; seed 42 alone works, all three reproduce the published result |

## Performance

| | accuracy | macro-F1 |
|---|---|---|
| round 1 (no neighbor context) | 0.845 | |
| final | 0.881 (95% CI 0.858 to 0.905) | 0.852 |

Per class F1: root cap 97.7, epidermis 89.8, exodermis 85.6, cortex 93.4,
endodermis 88.8, pericycle 86.5, stele 84.0, xylem 71.4, phloem 69.5.
Stele, xylem and phloem are the hard classes; most of their confusion is
among themselves.

## Author

Tran Chau (tnchau@vt.edu)