A napari plugin for spatial transcriptomics data analysis and visualization. This plugin provides tools for processing and analyzing spatial transcriptomics data using bio-photos, with a focus on cell aggregation detection, tissue segmentation, and data visualization.
- Cell Aggregation Analysis: Detect and analyze cell aggregates using OPTICS clustering algorithm
- Tissue Segmentation: Visualize gene signature scores across spatial coordinates and tissue segmentation
- Data Visualization: Interactive visualization of spatial transcriptomics data
- Data Export: Export processed data into multi-columns csv for further merging with anndata or seurat objects
You can install napari-stereoTis via [pip]:
pip install napari-stereoTis-
Start napari:
napari
-
Load the plugin from the Plugins menu
The plugin accepts CSV files with the following format:
- For cell aggregation: CSV with x,y coordinates (with header)
- For signature scoring: CSV with x,y coordinates and score values (with header)
- napari[all]
- numpy
- scikit-image
- opencv-python
- pandas
- matplotlib
Contributions are welcome! Please feel free to submit a Pull Request.
Distributed under the terms of the Apache License 2.0, "napari-stereoTis" is free and open source software.
If you encounter any problems, please file an issue along with a detailed description.