Current version: 1.0.0 (Orion)
A package for unified and scalable organism-wide cell annotation in single-cell and spatial transcriptomics.
Uses the Pan-human Azimuth neural network.
python>=3.9pipgit
To install the base version of the package (with CPU support only), run:
pip install panhumanpyor to install from GitHub, run:
pip install git+https://github.com/satijalab/panhumanpy.gitIf you require GPU acceleration for enhanced performance on compatible hardware, install the package with GPU dependencies:
pip install panhumanpy[gpu]or from GitHub:
pip install git+https://github.com/satijalab/panhumanpy.git#egg=panhumanpy[gpu]panhumanpy uses versioned models corresponding to major package releases. The package defaults to model 'v{i}' where i is the major package version. For panhumanpy 1.0.0 (Orion), the default model version is 'v1'. For most users, the default version is recommended. The user can also choose to use a different model version as outlined in the tutorial mentioned below.
Currently available model versions: 'v0', 'v1'
Model weights are hosted on Zenodo and downloaded automatically on first use, cached in ~/.cache/panhumanpy/. No manual download is required.
| Field | Detail |
|---|---|
| DOI | https://doi.org/10.5281/zenodo.20401417 |
| Models | v0, v1 |
| License | CC BY 4.0 |
panhumanpy includes a built-in crosswalk that maps Pan-human Azimuth cell type annotations to Cell Ontology (CL) terms. This mapping is versioned alongside the model and can be applied to annotation outputs via the map_to_cell_ontology function in ANNotate_tools or the map_to_cell_ontology method on AzimuthNN and AzimuthNN_base.
Crosswalk provenance:
| Field | Detail |
|---|---|
| Title | Crosswalk of Pan-human Azimuth Types annotated cells to Cell Ontology |
| Author | Aleix Puig-Barbe |
| Author ORCID | 0000-0001-6677-8489 |
| Reviewers | Bruce Herr II, Katy Borner, Jie Zheng |
| Reviewer ORCIDs | 0000-0002-6703-7647, 0000-0002-3321-6137, 0000-0002-2999-0103 |
| Data DOI | https://doi.org/10.48539/HBM727.TLKL.237 |
| Date | December 15, 2025 |
| Version | v1.1 |
For an introductory tutorial, please check out this notebook.
For more information on Pan-human Azimuth please visit our website.
A pre-print on the development and applications of Pan-human Azimuth is now on bioRxiv.