fidoptCellpose (cyto3)
Cellpose 3's generalist cyto3 model, trained on nine datasets among which the 2018 Data Science Bowl, run as the package's Cellpose class runs it at its defaults (grey, diameter 30), every mask one nucleus.
SegmentationCPUversion cellpose 3.1.1.2, models cyto3 and size_cyto3.npy of cellpose.org (sha256 2dc3087a, 87f91feb)HISTOLOGY, MICROSCOPYBSD-3-Clause
Run it
With its KonfAI app, at the benchmark's settings (the fidopt app repositories are private for now: a Hugging Face token with access opens them):
pip install konfai-apps konfai-apps infer fideus-labs/fidopt-segmentation:Cellpose_cyto3 -i image.nii.gz -o out
The app on Hugging Face: its model, its settings and how it is scored.
Results
| Dataset | # | Read by | Score | Failed | Time s |
|---|---|---|---|---|---|
| NuInsSeg, nuclei outlined by hand on H&E | Dice | 0.419 | 0 | 21 |
- Reference
- Stringer and Pachitariu, Nature Methods 2025; Stringer et al., Nature Methods 2021