README.md

metadata

title: >-
  RootScope: Cross-species Root Cell-Type Classification from Confocal
  Microscopy Images
emoji: 🌱
colorFrom: green
colorTo: blue
sdk: gradio
sdk_version: 5.49.1
app_file: app.py
pinned: false
license: mit
short_description: Classify root cell types across species from confocal TIFFs

RootScope web app

Web front end for RootScope. Upload a confocal root cross-section TIFF and get back a labeled overlay and a per-cell CSV. Every cell is segmented with Cellpose-SAM and assigned to one of nine cell types: root cap, epidermis, exodermis, cortex, endodermis, pericycle, stele, xylem, phloem.

How to use

1. Upload a raw confocal TIFF (not a mask). Pixel size is read from the OME metadata.
2. Optionally type the species name. It is not required; if given, it is checked against the species table shipped with the package.
3. Press Run. Segmentation and the DINOv2 embeddings run on the GPU; a 700x700 image with about 200 cells takes about 20 to 45 seconds.
4. Download the overlay image and the CSV of per-cell predictions.

One image at a time. For batches use the command line: rootscope --tif-dir.

Run it locally

conda activate rootscope
pip install gradio
python webapp/app.py

Model weights download from ct-tranchau/Rootscope on first use.

Author

Tran Chau (tnchau@vt.edu)