Data analysis and figure generation for the SpotSweeper-py manuscript
This repository contains the data analysis Jupyter notebooks used in the SpotSweeper-py manuscript.
It is intended for reproducibility of the manuscript results and does not contain the SpotSweeper-py software package itself.
Title: SpotSweeper-py: spatially-aware quality control metrics for spatial omics data in the Python ecosystem
Authors: Xingyi Chen, Michael Totty, Stephanie C. Hicks
Venue: bioRxiv (2025)
DOI: https://doi.org/10.64898/2025.12.06.692760
The SpotSweeper-py software package is maintained in a separate repository:
https://github.com/danielchen05/spotsweeper_py
It is also available on PyPI:
https://pypi.org/project/spotsweeper/
All analysis is organized as Jupyter notebooks.
| Notebook | Description |
|---|---|
Visium.ipynb |
Analysis of 10x Visium datasets; comparison of global vs local QC metrics |
VisiumHD.ipynb |
Analysis of 10x Visium HD data at higher spatial resolution |
Each notebook is intended to be run top-to-bottom after downloading the required data and setting appropriate paths.
Raw datasets used in the manuscript are not stored directly in this repository due to size constraints.
The datasets can be downloaded from the 10x Genomics website:
- Visium: https://www.10xgenomics.com/datasets/gene-and-protein-expression-library-of-human-breast-cancer-cytassist-ffpe-2-standard
- Visium HD: https://www.10xgenomics.com/datasets/visium-hd-cytassist-gene-expression-libraries-human-breast-cancer-ffpe-if
- Download datasets from the sources listed above.
- Extract them locally if needed.
- Update file paths in the corresponding notebooks if necessary.
Notes on preprocessing are documented within each notebook.
Downstream analyses expect an AnnData object; feel free to use your preferred method to load the data. (especially for the Visium HD data)
For questions related to the analysis or manuscript figures, please contact:
Xingyi (Daniel) Chen — xchen274@jh.edu
For questions related to the SpotSweeper-py software package, see:
https://github.com/danielchen05/spotsweeper_py