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)