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.
Data Setup¶
- 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 your datasets via Zenodo.
- Load External Data: Directly load a dataset from a URL (S3 or Zenodo) into the viewer.
Data Library Setup¶
- 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.
Map View¶
- 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.
Explore Gene¶
- 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.
Investigate Factor¶
- How to View Marker Genes for One Factor: Open the marker gene table/chart for one specific factor.
- How to Interact with Spatial Factor(s): Highlight specific spatial factors (e.g., cell types or tissue domains) and customize their visualization on the map.
ROI Analysis¶
- 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.
Data Inspection¶
- How to Inspect a Spot: Click or hover over spots to view detailed molecular or factor data.
Filter & Search¶
- How to Use Code Filter: Write multi-condition code expressions to filter any data table by field values, text patterns, or gene lists.
Use Alias¶
- How to Add Alias: Add Manual, Upload, or AI-inferred aliases to a factor layer, or reset back to the curated aliases.
- How to Prepare Curated Alias: Prepare an alias file to use as the default curated alias for a factor layer.
- How to Prepare AI Alias: Prepare an alias file to use as the AI-inferred alias for a factor layer.
- 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.
Save & Share¶
- 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.