SMURF: Segmentation and Manifold UnRolling Framework¶
Welcome to SMURF!
SMURF performs soft segmentation of VisiumHD data, facilitating the creation of a cells*genes anndata object. SMURF uses high-resolution images from VisiumHD for nuclei segmentation and then assigns the transcripts recovered from each capture ‘spot’ to a nearby cell. See preprint paper for more details.
If you find a model useful for your research, please cite the following:
@article{guo2025smurf,
title={SMURF Reconstructs Single-Cells from Visium HD Data to Reveal Zonation of Transcriptional Programs in the Intestine},
author={Guo, Juanru and Sarafinovska, Simona and Hagenson, Ryan and Valentine, Mark and Dougherty, Joseph and Mitra, Robi David and Muegge, Brian D},
journal={bioRxiv},
pages={2025--05},
year={2025},
publisher={Cold Spring Harbor Laboratory}
}
Installation
Click here to view a brief SMURF installation guide and prerequisites.
Tutorials
End-to-end tutorials showcasing key features in the package.
User guide
User guide provides some detail information of SMURF.
API reference
Detailed descriptions of SMURF API and internals.
GitHub
Ask questions, report bugs, and contribute to SMURF at our GitHub repository.