stereopy 1.6.1

Spatial transcriptomic analysis in python.

Stereopy: Spatial Transcriptomics Analysis in Python

Installation - Quick start - Documentation - API

Stereopy is a fundamental and comprehensive tool for mining and visualization based on spatial transcriptomics data, such as Stereo-seq (spatial enhanced resolution omics sequencing) data. More analysis will be added here, either from other popular tools or developed by ourselves, to meet diverse requirements. Meanwhile, we are still working on the improvement of performance and calculation efficiency.

Discussion

Please use GitHub issues tracker for reports and discussions of:

• Bug reports
• Document and data issues
• Feature requirements
• ...

Contribution

Stereopy is in a stage of rapid development so that we will carefully consider all aspects of your proposal. We hope future input will be given by both users and developers.

Details to contributing.

Citing Stereopy

@Article{Fang2025,
author={Fang, Shuangsang and Xu, Mengyang and Cao, Lei and Liu, Xiaobin and Bezulj, Marija and Tan, Liwei and Yuan, Zhiyuan and Li, Yao and Xia, Tianyi and Guo, Longyu and Kovacevic, Vladimir and Hui, Junhou and Guo, Lidong and Liu, Chao and Cheng, Mengnan and Lin, Li'ang and Wen, Zhenbin and Josic, Bojana and Milicevic, Nikola and Qiu, Ping and Lu, Qin and Li, Yumei and Wang, Leying and Hu, Luni and Zhang, Chao and Kang, Qiang and Chen, Fengzhen and Deng, Ziqing and Li, Junhua and Li, Mei and Li, Shengkang and Zhao, Yi and Fan, Guangyi and Zhang, Yong and Chen, Ao and Li, Yuxiang and Xu, Xun},
title={Stereopy: modeling comparative and spatiotemporal cellular heterogeneity via multi-sample spatial transcriptomics},
journal={Nature Communications},
year={2025},
month={Apr},
day={21},
volume={16},
number={1},
pages={3741}
}