metadata
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. 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)