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Vignettes

Explore a series of tutorials that help you learn CartLoader — from quick, getting‑started examples to processing full‑scale ST datasets.

To view details of a specific module, see Reference section.

Quick Start

If you’re new to CartLoader, start with the Quick Start tutorial, a beginner‑friendly walkthrough using a small mouse hippocampus dataset to core CartLoader functions.

  • Quick Start
    Quick Start Tutorial

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Getting Started per Platform

These tutorials demonstrate how to run CartLoader on a variety of ST platforms using small, representative datasets.

Warning

For consistency, we use mouse hippocampus when available.

Each tutorial begins with data in the platform’s native format.

Sequencing-based Platforms

  • example1
    SeqScope Starter Guide

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  • example2
    10x Visium HD Starter Guide

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  • example3
    StereoSeq Starter Guide

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  • example3
    Pixel-seq Starter Guide

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Imaging-based Platforms

  • example3
    10x Xenium Starter Guide

    Read

  • example3
    Vizgen MERSCOPE Starter Guide

    Read

  • example3
    CosMX SMI Starter Guide

    Read

End‑to‑end workflows by platform

These examples show how to process real‑world ST datasets from different platform using end-to-end workflow from CartLoader.

  • example3
    10x Xenium Pipeline Guide

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  • example3
    Visium HD Pipeline Guide

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Multi‑Sample Analysis

Warning

This section is under active development.

Upcoming content will cover how to process multiple samples in a single batch, including cross‑sample analysis.