stEDGE 1.1.1

Edge-guided multiscale reconstruction of hierarchical spatial domains and transition interfaces in spatial transcriptomics

stEDGE: Edge-guided multiscale reconstruction of hierarchical spatial domains and transition interfaces in spatial transcriptomics

Overview

stEDGE is an edge-guided and interpretable framework for reconstructing multiscale tissue architecture from spatial transcriptomics data. Instead of treating tissues as flat spatial partitions, stEDGE explicitly models local boundary probability and domain transition intensity to identify stable compartments, transition-rich interfaces, and hierarchical spatial states.

stEDGE integrates four major components: consensus-based boundary modeling, edge-guided fine-domain reconstruction, transition-aware hierarchy construction, and tree-guided gene program interpretation.

Using stEDGE, you can:

• Reconstruct fine-grained spatial domains by modeling local boundary probability and growing domains from low-boundary core regions.

• Identify transition-rich interfaces using boundary probability, gradient signals, and domain transition indices.

• Build multiscale tissue hierarchies across fine, domain, and coarse spatial levels using domain graphs and hierarchy trees.

• Interpret spatial gene programs with tree-guided gene attribution, distinguishing shared parent-level identity from branch-specific molecular programs.

• Analyze diverse spatial transcriptomics datasets, including Visium, Slide-seqV2, Xenium, and other spatial omics platforms.

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Installation

We recommend installing stEDGE in a clean conda environment.

Step 1. Create a conda environment

conda create -n stEDGE python=3.12.5
conda activate stEDGE

Step 2. Install dependency packages

pip install -r requirements.txt

Step 3. Install stEDGE

For local installation, we recommend editable mode:

pip install -e .

Alternatively, you can install stEDGE using the setup script:

pip install setuptools==58.2.0
python setup.py build
python setup.py install

The environment configuration is then completed.

Tutorials

For installation instructions and step-by-step tutorials, please refer to the online documentation:

https://stedge-tutorials.readthedocs.io/en/latest/

Tutorial source repository:

https://github.com/yihe-csu/stEDGE_Tutorials

Citation

If you use stEDGE in your work, please cite:

He, Y. stEDGE enables edge-guided multiscale reconstruction of hierarchical spatial domains and transition interfaces in spatial transcriptomics. 2026.

Citation information will be updated upon publication.