User Manual Overview¶

Welcome to the CartoScope User Manual! This guide is designed to help you navigate and utilize the features of the CartoScope effectively.

The manual is organized into the following main sections:

Data Exploration¶

Learn how to find and load data.

Overview: A summary of the different ways to access and load data into CartoScope.
Explore Available Collections: Browse and search for datasets organized within specific collections.
Explore Ready-to-Use Data: Access the CartoScope catalog to find and load high-quality public datasets.
Load Your Own Data: Instructions for loading datasets from external URLs (S3, Zenodo) or local files.
Preview Datasets: Learn how to verify dataset metadata and content before fully loading it.

Understand the core interface where you will spend most of your time exploring data.

Overview: An introduction to the main interface layout, including the sidebar, map view, and toolbars.
Top Bar: Guide to the top navigation bar, including global settings and quick actions.
Layer Drawer: Manage the visibility, opacity, and ordering of different data layers.
Central Map View: Interact with the visualization, including zooming, panning, and selecting features.
Gene Drawer: Tools for searching, filtering, and visualizing gene expression patterns.
Factor Drawer: Explore inferred spatial factors, clusters, and their distributions.
ROI Drawer: Create, manage, and analyze user-defined Regions of Interest.
Inspector Drawer: View detailed molecular profiles and properties for specific spots or cells.

Discover how to save your work and share it with others.

Overview: A summary of the available options for saving and sharing your analysis.
Share via Link: Generate a direct URL to share your current view state with others.
Bookmark Workspace: Save your entire workspace configuration, including layers and ROIs, as a bookmark.
Export Map View: Capture and download high-resolution screenshots of your current map view.