User Manual Overview¶

Welcome to the CartoScope User Manual. This guide provides detailed information on all interface components and tools available for exploring spatially resolved transcriptomics data.

Interface¶

CartoScope's interface is organized into several key areas, each serving a specific purpose in your data exploration workflow.

CartoScope Interface

1. Top Bar. Global controls, redirect buttons, dataset name, and export options.

2. Layer Drawer. The central hub for managing your visualization layers. Here you can toggle visibility, adjust opacity, and configure settings for background images, factors, and gene expression layers.

3. Map View. The main visualization area where you interact with the spatial data. It supports panning, zooming, and rotating to inspect tissues at varying resolutions.

4. Analysis Drawer. The analysis drawer is displayed on the right side of the interface. The analysis drawer includes the components below.

Gene Drawer: View the gene list (including names and expression counts) and visualize the spatial distribution of specific genes on the map.
Factor Drawer: Explore available factor layers—including spatial factors inferred by tools like FICTURE, cell analysis results, and other user-defined factors—to uncover underlying biological patterns. The screenshot above displays the Factor Drawer.
ROI Drawer: Define Regions of Interest (ROIs) to perform localized analysis and export data for specific tissue areas.
Inspector Drawer: Inspect detailed information for specific pixels or spots under your cursor, such as gene expression counts and factor weights.