SpaIM

Single-cell Spatial Transcriptomics Imputation via Style Transfer

📄 Read the Paper in Nature Communications

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We introduce SpaIM, a novel style transfer learning model that leverages scRNA-seq data to accurately impute unmeasured gene expressions in spatial transcriptomics (ST) data. SpaIM separates scRNA-seq and ST data into data-agnostic contents and data-specific styles, capturing commonalities and unique differences, respectively. By integrating scRNA-seq and ST strengths, SpaIM addresses data sparsity and limited gene coverage, outperforming existing methods across 53 diverse ST datasets. It also enhances downstream analyses like ligand-receptor interaction detection, spatial domain characterization, and differentially expressed gene identification.

Getting Started

Environment

To get started with SpaIM, please follow the steps below to set up your environment:

git clone https://github.com/QSong-github/SpaIM
cd SpaIM
conda env create -f environment.yaml
conda activate SpaIM

Datasets

All datasets used in this study are publicly available.

• Data sources and detailed information are provided in Supplementary_Table_1. After downloading the data, please refer to the processing steps outlined in Data Processing README.txt and execute the code in Data Processing.py to perform the analysis and obtain clustering results.

• All processed datasets can be downloaded at Zenodo and Synapse.

The datasets should be organized in the following structure:

|-- dataset
|-- Dataset1
|-- Dataset2
|-- ......
|-- Dataset52
|-- Dataset53

SpaIM Training and Testing

Train all 53 datasets with a single command:

chmod +x ./*
./run_SpaIM.sh

The trained models and metric results will be saved in the following directories:

./SpaIM_results/Dataset1/

SpaIM Inference

Run the following command to perform inference:

cd test
python SpaIM_imputation.py

The inference results will will be saved in './SpaIM_results/Dataset1/impute_sc_result_%d.pkl'.

Reference

If you find this project is useful for your research, please cite:

Li B, Tang Z, Budhkar A, Liu X, Zhang T, Yang B, Su J, Song Q. SpaIM: single-cell spatial transcriptomics imputation via style transfer. Nature Communications. 2025 Aug 23;16(1):7861.

Acknowledgments

Our code is based on the neural-style. Special thanks to the authors and contributors for their invaluable work.