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Data Exploration & Loading Overview

CartoScope supports multiple data access pathways depending on whether you are exploring public atlas data or analyzing your own lab datasets. This overview compares the data loading options and session types.

Quick Start

If you are new to CartoScope, start with Explore Ready-to-Use Data or Explore Available Collections to explore example datasets instantly.

1. Data Access Pathways Comparison

Access Option Data Source Setup Required Best For Related Manual Page
Public Datasets CartoStore Atlas None (1-click launch) Exploring published spatial datasets across species and tissues Explore Ready-to-Use Data
Collections CartoStore Atlas None (1-click launch) Exploring curated dataset groups (e.g. disease models, organ cohorts) Explore Collections
External URL Loading S3, Zenodo, HTTP catalog.yaml or direct link Quick loading of custom single or multi-sample datasets Load Your Own Data
Custom Data Library User-hosted HTTP/S3 Parquet index (metadb/) Managing and browsing large collections of custom lab datasets Load Your Own Data

2. Session Type Comparison: Single-Sample vs. Multi-Sample

When loading data, CartoScope supports two distinct session modes:

Single-Sample Sessions

  • Focus: In-depth, high-resolution exploration of a single tissue section.
  • Key Features: Full Layer Drawer control, precision zoom/rotation numerical readouts in the Map View Summary panel, spot/cell inspection, and single-sample ROI differential expression.
  • Entry Points: Direct 1-click launch from the Public Catalog or direct URL loading (catalog.yaml).

Multi-Sample Cohort Sessions

  • Focus: Comparative spatial analysis across multiple tissue slides (e.g. Control vs. Treated, time-series, or replicate slides).
  • Key Features: Synchronized grid navigation, camera lock/unlink, sample labeling, Chi-squared & DESeq2-inspired statistical models, volcano plots, and slot drag-and-drop reordering.
  • Entry Points: Launched via the Set Up Multi-Sample Session dialog using a multi-catalog.yaml or selecting multiple catalog datasets.

Single-Sample vs. Multi-Sample Guidance

For a detailed breakdown of benefits and requirements—including why multi-sample sessions require datasets analyzed together in a joint pipeline—see the FAQ: Should I Choose a Single-Sample or Multi-Sample Session?.

Related Pages

Concepts

Manual Pages