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

RootScope uses Cellpose-SAM to segment every cell and describes each one with morpho-topological features and fine-tuned DINOv2 embeddings. Classification is refined through an iterative process in which predictions from neighboring cells are fed back as new features, updating every label until the classification converges. Each cell is then assigned to one of nine anatomical types.

github · model weights · model card

Input TIFF

Preview

Upload a root-tip TIFF to begin.

Microns per pixel

Read from the file's metadata when present. This is not optional. The 1.0 default distorts every size-derived feature.

Model to display

One LightGBM (three training seeds averaged inside); this is the published result.

Species (optional)

Not required. If given, it is checked against the species table: for a training species it settles whether the root has an exodermis; otherwise the image decides.

_{Free GPU time is per visitor, per day: 2 minutes signed out, 5 minutes with a free Hugging Face account. One image costs roughly 30 seconds. Sign in and reload if you run out.}

Predicted cell types

■ root cap ■ epidermis ■ exodermis ■ cortex ■ endodermis ■ pericycle ■ xylem ■ phloem ■ stele

Cells per type

Example images (click one, then press Run)