panhumanpy 1.0.0

A Python package for automated cell type annotation in scRNA-seq using Azimuth Neural Network.

panhumanpy

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.

Prerequisites

• python >=3.9
• pip
• git

Installation

To install the base version of the package (with CPU support only), run:

pip install panhumanpy

or to install from GitHub, run:

pip install git+https://github.com/satijalab/panhumanpy.git

If 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]

Model Versions

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

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

Cell Ontology Mapping

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

Tutorial

For an introductory tutorial, please check out this notebook.

For more information on Pan-human Azimuth please visit our website.