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:

• SeqScope
• Stereo-seq
• Pixel-seq
• 10x Visium HD
• 10x Xenium
• Vizgen MERSCOPE
• CosMx SMI

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 FICTURE: Run analysis across multiple samples.

Next

Once processed, your data needs to be hosted on a cloud storage service accessible to CartoScope.

Please follow our detailed guides for your preferred hosting provider:

• Host on AWS S3: Recommended for high performance and private data.
• Host on Zenodo: Recommended for permanent archiving and public sharing (DOI).