How-To Guides Overview¶

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

Account Setup¶

How to Create a New Account: Sign up for a new CartoScope account to manage your data.

How to Prepare your Data: Format and process your spatial omics data for import.
How to Host your Data in AWS: Set up an S3 bucket to host your datasets.
How to Host your Data in Zenodo: Archive and share your datasets via Zenodo for public access.
Load External Data: Directly load a dataset from a URL (S3 or Zenodo) into the viewer.

How to Prepare a Data Library: Process datasets and generate the Parquet metadata index using CartoMint.
How to Connect Your Data Library in CartoScope: Register a hosted library in CartoScope and switch between libraries.

How to Add Layers: Organize your map by adding background, genes, or factor layers.
How to Orient the View: Learn how to rotate, flip, and navigate the spatial map.
How to Set the Map View via the Scaling Settings: Read and edit zoom, rotation, pitch, and coordinate range from the Map View Summary panel.

How to Add a Gene: Search for and visualize the expression pattern of a specific gene.
How to Add a Gene Group: Combine multiple genes into a single layer to view their aggregate expression.

How to Highlight a Factor: Focus on specific spatial factors (e.g., cell types or tissue domains).
How to Add Alias: Add Manual, Upload, or AI-inferred aliases to a factor layer, or reset back to Curated aliases.
How to Upload Alias: Prepare a valid alias TSV file and upload it to the active factor layer.
How to Load AI Alias: Load the AI-inferred alias table for the active factor layer when it is available.
How to Change Factor Color: Customize the color palette of factor layers for better visualization.

How to Create a ROI: Draw and define Regions of Interest (ROIs) on the map.
How to Load Existing ROI: Import previously saved ROI files into your current session.
How to Refine a ROI: Edit the boundaries or position of an existing ROI.
How to Compare two ROIs: Analyze and compare expression data between two different regions.

How to Use Code Filter: Write multi-condition code expressions to filter any data table by field values, text patterns, or gene lists.

How to Inspect a Spot: Click or hover over spots to view detailed molecular or factor data.

How to Create a Bookmark: Save your current view, layers, and settings as a shareable bookmark.
How to Export Map View: download high-resolution images of your current map view.
How to Share via Link: Generate a quick link to share your exact view state.
How to Export Gene Data: Download gene expression matrices or lists for your analysis.
How to Export Factor Data: Export the results of spatial factor analysis.
How to Export ROI Data: Download the data specific to your defined Regions of Interest.