napari-stereoTis 0.1.0

Used to mask cells or tissues for spatial transcriptomes

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

• numpy

• scikit-image

• opencv-python

• pandas

• matplotlib

License

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

Links

Source Code: https://github.com/secretloong/napari-stereoTis