Common Questions¶

General¶

Which browser should I use?¶

CartoScope is a modern web application that relies on advanced web technologies (WebGL). For the best experience, we strongly recommend using Google Chrome, Microsoft Edge, or other Chromium-based browsers. Safari and Firefox are supported but might have performance limitations with very large datasets.

Terminology¶

What is a Gene Group?¶

A Gene Group allows you to combine multiple genes into a single layer on the map. This is useful when you want to visualize the aggregate expression of a set of related genes (e.g., cell type markers) as one coherent visual element, sharing the same color scale.

What types of layers can I add?¶

Gene: Spatial plots of individual gene expression.
Gene Group: A combination of multiple genes into a single layer.
Factor: Result layers from spatial factor analysis (e.g., FICTURE).
Background (BG): Histology images (H&E, DAPI) or other base maps.
ROI: User-defined Regions of Interest.

Data & Hosting¶

Why is my external dataset not loading?¶

Check the URL: Ensure there are no typos.
Access Permissions: Ensure you have permission to access the file.
CORS Issues: You must configure your cloud storage (AWS S3, etc.) to allow CORS requests from https://seqscope.github.io. See How to Host on AWS S3 for details.

What data can I export?¶

Gene/Factor: Expression matrices, DE results, Summary TSVs.
ROI: GeoJSON geometries, raw transcript lists.
Map: High-res screenshots (PNG/PDF).

What is the difference between Public and Unlisted bookmarks?¶

Public: Listed in the public catalog visible to everyone.
Unlisted: Accessible only via the shared link. Not listed in catalogs.

Performance¶

Why is my data taking so long to load?¶

Initial Load: Metadata fetching can take a moment.
Large ROIs: Avoid "Load all data" for large areas (see Detailed Guide).
Network: Check your internet speed.

The map is laggy¶

Hardware Acceleration: Enable this in your browser settings.
Hide Layers: Turn off visibility for layers you aren't using.