napari-stereoTis 0.3.0

Used to mask cells or tissues for spatial transcriptomes

napari-stereoTis

Description

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.

Features

• 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

Installation

You can install napari-stereoTis via [pip]:

pip install napari-stereoTis

Usage

1. Start napari:

   napari
   

2. Load the plugin from the Plugins menu

Input Data Format

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)

Requirements

• napari[all]
• numpy
• scikit-image
• opencv-python
• pandas
• matplotlib

Contributing

Contributions are welcome! Please feel free to submit a Pull Request.

License

Distributed under the terms of the Apache License 2.0, "napari-stereoTis" is free and open source software.

Issues

If you encounter any problems, please file an issue along with a detailed description.