SpaGCN Modern

spagcn-modern is an independently maintained fork of SpaGCN, a graph convolutional network for identifying spatial domains and spatially variable genes from gene expression, spatial coordinates, and histology.

The distribution keeps the original SpaGCN import package and numerical API while supporting current Python, SciPy, Scanpy, and AnnData releases. Graph initialization uses the maintained Leiden implementation built into igraph.

Installation

pip install spagcn-modern

The import name remains unchanged:

import SpaGCN

Maintenance scope

This repository contains only the maintained Python distribution. Tutorials, sample outputs, prebuilt distributions, and paper assets remain available in the original repository and are not runtime dependencies.

Compatibility fixes in this fork include:

• current SciPy sparse-array conversion through toarray();
• corrected use_raw behavior in plot_log_exp;
• mathematically correct DEC soft assignments using the Student's t kernel;
• native sparse PCA plus cached resolution-search preprocessing;
• bounded Gaussian-kernel workspaces and zero-copy float32 tensor conversion;
• minimal runtime dependency metadata derived from imports;
• maintained igraph Leiden initialization instead of the obsolete Louvain extension;
• isolated wheel builds and sparse-data smoke tests in CI.

Citation

Please cite the original SpaGCN publication:

Hu J, et al. SpaGCN: Integrating gene expression, spatial location and histology to identify spatial domains and spatially variable genes by graph convolutional network. Nature Methods (2021).

Attribution and license

SpaGCN was created by Jian Hu and collaborators. This maintained fork preserves the original MIT license and records its upstream base in NOTICE.md.