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. Read the documentation for detailed tutorials.
Quickstart
import cellpin
from torch.utils.data import DataLoader
sc_ds, st_ds = cellpin.pp.setup_data(sc_adata, st_adata)
model = cellpin.CellPin(sc_ds)
model.fit(sc_ds)
loader = DataLoader(st_ds, batch_size=256, shuffle=False)
adata_out = model.impute(loader, obs_adata=st_adata)
Installation
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]"
Documentation
Full documentation, tutorials, and API reference: cellpin.readthedocs.io
Citation
If you use cellpin in your research, please cite:
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
* Shared first authorship
@article{putze2026cellpin,
title = {Cellpin enables reference-based imputation and denoising of spatial transcriptomes},
author = {Putze, Philipp and Lucarelli, Daniele and Wellappili, Deelaka and Bahrami, Mojtaba and Luecken, Malte D. and Theis, Fabian J. and Saur, Dieter},
journal = {bioRxiv},
year = {2026},
doi = {10.64898/2026.06.02.729566},
url = {https://doi.org/10.64898/2026.06.02.729566}
}
1 maintainer
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Source Distribution
Built Distribution
Filter files by name, interpreter, ABI, and platform.
If you're not sure about the file name format, learn more about wheel file names.
Copy a direct link to the current filters
File details
Details for the file cellpin-0.2.0.tar.gz.
File metadata
- Download URL: cellpin-0.2.0.tar.gz
- Upload date:
- Size: 24.4 MB
- Tags: Source
- Uploaded using Trusted Publishing? Yes
- Uploaded via: twine/6.1.0 CPython/3.13.14
File hashes
| Algorithm | Hash digest | |
|---|---|---|
| SHA256 |
50c2aa469e9a0016e824724618e0243cc41b6101d4a9dd65765da95f1445ab52
|
|
| MD5 |
7486235252b681d8ac172d6fef3ec644
|
|
| BLAKE2b-256 |
7122cee7ef944aab34ed9a2c49a0110cfc4db7789de05c05851db6ec98ff404e
|
Provenance
The following attestation bundles were made for cellpin-0.2.0.tar.gz:
Publisher:
release.yml on Saur-Lab/cellpin
-
Statement:
-
Statement type:
https://in-toto.io/Statement/v1 -
Predicate type:
https://docs.pypi.org/attestations/publish/v1 -
Subject name:
cellpin-0.2.0.tar.gz -
Subject digest:
50c2aa469e9a0016e824724618e0243cc41b6101d4a9dd65765da95f1445ab52 - Sigstore transparency entry: 2280817133
- Sigstore integration time:
-
Permalink:
Saur-Lab/cellpin@9bc9cdae2ecda4176a43c871e346d04fe31b48b8 -
Branch / Tag:
refs/tags/v0.2.0 - Owner: https://github.com/Saur-Lab
-
Access:
public
-
Token Issuer:
https://token.actions.githubusercontent.com -
Runner Environment:
github-hosted -
Publication workflow:
release.yml@9bc9cdae2ecda4176a43c871e346d04fe31b48b8 -
Trigger Event:
release
-
Statement type:
File details
Details for the file cellpin-0.2.0-py3-none-any.whl.
File metadata
- Download URL: cellpin-0.2.0-py3-none-any.whl
- Upload date:
- Size: 51.3 kB
- Tags: Python 3
- Uploaded using Trusted Publishing? Yes
- Uploaded via: twine/6.1.0 CPython/3.13.14
File hashes
| Algorithm | Hash digest | |
|---|---|---|
| SHA256 |
2c373c19ab3aa77837effa1879212b67ed625d77500afeee8fa097ed9811a7f4
|
|
| MD5 |
962bd1e1554ee35acdbbc0fe79255072
|
|
| BLAKE2b-256 |
3c31b9f1eae690996eefa27c7d63c9b1350b66f34f20fbf07bc8797ad97784e5
|
Provenance
The following attestation bundles were made for cellpin-0.2.0-py3-none-any.whl:
Publisher:
release.yml on Saur-Lab/cellpin
-
Statement:
-
Statement type:
https://in-toto.io/Statement/v1 -
Predicate type:
https://docs.pypi.org/attestations/publish/v1 -
Subject name:
cellpin-0.2.0-py3-none-any.whl -
Subject digest:
2c373c19ab3aa77837effa1879212b67ed625d77500afeee8fa097ed9811a7f4 - Sigstore transparency entry: 2280817157
- Sigstore integration time:
-
Permalink:
Saur-Lab/cellpin@9bc9cdae2ecda4176a43c871e346d04fe31b48b8 -
Branch / Tag:
refs/tags/v0.2.0 - Owner: https://github.com/Saur-Lab
-
Access:
public
-
Token Issuer:
https://token.actions.githubusercontent.com -
Runner Environment:
github-hosted -
Publication workflow:
release.yml@9bc9cdae2ecda4176a43c871e346d04fe31b48b8 -
Trigger Event:
release
-
Statement type:
