cellpin

Cellpin is a lightweight probabilistic model that reconstructs and denoises spatial transcriptomes from single-cell RNA-seq references. It enables transcriptome-wide imputation, robust atlas-to-spatial label-transfer, and improved biological interpretation of both targeted-panel and full-transcriptome spatial datasets.

Installation

Python 3.11 or newer is required.

pip

pip install cellpin

uv

uv pip install cellpin

For SpatialData support add the spatial extras:

pip install "cellpin[spatial]"
# or
uv pip install "cellpin[spatial]"

Release notes

See the changelog.

Contact

If you found a bug or have a feature request, please use the issue tracker.

Citation

Putze P*, Lucarelli D*, Wellappili D, Bahrami M, Luecken MD, Theis FJ, Saur D. Cellpin enables reference-based imputation and denoising of spatial transcriptomes. bioRxiv 2026.06.02.729566. doi: 10.64898/2026.06.02.729566