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How to Prepare a Data Library

Concept

Step 1. Prepare Your Datasets

Process your raw spatial omics data into the CartoScope-compatible format using CartLoader.

See How to Prepare your Data for detailed instructions.

Step 2. Host Your Data on AWS S3

Upload the processed datasets to an AWS S3 bucket so they are accessible via HTTPS.

See How to Host Data in AWS for the required bucket policy and CORS configuration.

Step 3. Generate the Library Metadata with CartoMint

CartoMint is the official tool for generating the metadata index files that CartoScope reads to populate a Data Library. It scans your hosted datasets, reads their catalog.yaml files, and produces a metadb/ folder.

Refer to the CartoMint documentation for installation and usage instructions.

Output

After running CartoMint, you will have a metadb/ folder:

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metadb/
├── datasets.parquet       # catalog of all datasets (required)
├── collections.parquet    # collection groupings (optional)
└── genes.parquet          # gene search index (optional)

Upload this metadb/ folder to your S3 bucket. The URL to this folder is the library root URL you will use in the next step.

Next Step

How to Connect Your Data Library — register the library root URL in CartoScope.