cuspa: GPU spatial operations for spatial omics

cuspa assigns transcript coordinates to cell polygons and builds sparse cells-by-genes count matrices on the GPU. Geometry is stored in flat GeoArrow-style buffers. GeoPandas and SpatialData inputs are converted before GPU computation.

Installation

Install the prebuilt wheel for your CUDA major version:

[uv] pip install cuspa-cu12  # CUDA 12
[uv] pip install cuspa-cu13  # CUDA 13

Both distributions provide the cuspa Python package; install only one per environment. The optional adapters are extras, for example [uv] pip install "cuspa-cu12[geopandas]"; geoarrow and spatialdata work the same way.

cuspa requires Python 3.12 or newer, a compatible NVIDIA GPU and driver, a CUDA 12 or CUDA 13 runtime, and CuPy or CUDA-enabled PyTorch. Install the CuPy or PyTorch package for your CUDA environment separately. Aggregation and I/O adapters currently require CuPy.

To build from source instead, install the cuspa source distribution. This requires the matching CUDA toolkit and a C++17 compiler:

[uv] pip install cuspa

See the installation guide for wheel targets and source-build details.

Usage

import cuspa as cs

polys = cs.io.from_spatialdata(sdata, "cell_boundaries")
tx = cs.io.transcripts_from_spatialdata(sdata, "transcripts")

csr = cs.tl.aggregate_to_cells(
    [(tx.xy, tx.gene_ids)],
    polys,
    num_genes=len(tx.gene_names),
)

Documentation

See the documentation for installation, usage, geometry input, and the API reference.

Contributing

External contributions are open through pull requests. Report bugs and propose changes through GitHub Issues. See CONTRIBUTING.md for the contribution process. All project participants must follow the Code of Conduct.

Security

Do not report vulnerabilities through public GitHub issues. See SECURITY.md for NVIDIA's private reporting channels.

License

cuspa is licensed under Apache-2.0. See LICENSE.