How to Prepare Your Own Data for CartoScope?¶
This guide explains how to prepare your own spatial omics datasets for use in CartoScope.
CartoScope requires data to be processed and formatted specifically for efficient streaming. We provide CartLoader, a dedicated pipeline tool, to handle this processing.
1. Install CartLoader¶
Follow the official installation instructions to install CartLoader on your local machine or server.
2. Run the Pipeline¶
CartLoader supports various spatial transcriptomics platforms. Choose the instructions relevant to your data source:
Platform-Specific Tutorials
Follow these step-by-step tutorials to convert your raw data, run FICTURE analysis, and package the results into PMTiles:
If you need to perform specific tasks outside the standard pipeline, refer to the advanced guides:
Advanced Processing Tasks
- Import Cell Segmentation: Incorporate custom cell boundaries.
- Import Morphology Images: Align and deploy histology images.
- Import Square Bins: Import 8x8 µm or 16x16 µm bin analysis results.
- Multi-Sample Analysis: Run analysis across multiple samples. See What Is Multi-Sample Analysis? for why you'd want this.
Related Pages
Concepts
Manual Pages
How-to Guides