How-To Guides

This section provides step-by-step instructions for common tasks in CartoScope.

Data Setup

• Prepare Data: Process raw spatial omics data for CartoScope.
• Host Data on AWS S3: Host your processed data on AWS S3.
• Host Data on Zenodo: Archive and share your data via Zenodo.
• Load External Data: Load datasets from external URLs.

Map View

• Add Layers: Add background, gene, or factor layers to the view.
• Orient the View: Navigate, rotate, and flip the map view.

Explore Gene

• Add a Single Gene: Visualize expression of a single gene.
• Add a Gene Group: Visualize collective expression of multiple genes.

Investigate Factor

• Highlight a Factor: Visualize and highlight specific spatial factors.
• Change Factor Color: Customize colors for factor layers.

ROI Analysis

• Create an ROI: Define regions of interest using drawing tools.
• Load Existing ROI: Import ROIs from previously saved files.
• Refine an ROI: Edit the shape or position of an existing ROI.
• Compare Two ROIs: Perform comparative analysis between two regions.

Data Inspection

• Inspect a Spot: View detailed molecular profiles for specific locations.

Save & Share

• Share via Link: Share your current view via a direct URL.
• Create a Bookmark: Save your workspace state and share it.
• Export Map View: Capture high-quality images of the current map view.
• Export Gene Data: Download gene expression data.
• Export Factor Data: Download factor analysis results.
• Export ROI Data: Download data for defined regions of interest.