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Explore Available Data in CartoScope

CartoScope offers a growing number of public datasets for free access and exploration. These datasets span diverse species, tissues, conditions, and technologies. Each dataset includes raw ST data, FICTURE analysis results, and morphological images (with cell analysis results where available).

Functionality

The Data Catalog serves as a centralized hub for discovering and accessing the spatial omics datasets hosted in CartoStore. Those datasets were prepared to be ready-to-use for immediate interactive exploration in CartoScope.

It enables users to:

  • Browse Collections: Navigate datasets grouped by species, tissue, disease, or technology.
  • Search & Filter: Quickly locate relevant data using keywords or specific criteria filters (e.g., technology platform, organism).
  • Direct Access: Launch datasets directly into the CartoScope viewer for immediate exploration.

Collections

Datasets are grouped into collections based on their species, tissues, conditions, and technologies.

Collections

  1. Collapse filtering panel: This is a toggle button to collapse the filtering panel.
  2. Number of collections: Displays the count of collections (e.g., "10/30" indicates 10 collections match the current filter out of 30 total).
  3. Search and filtering options: This section contains a search bar and a list of filter options.
  4. Collection Header: Collections can be sorted by each column name by clicking the column name. For example, in the example screenshot, the collections can be sorted by the updated date.
  5. Collection Name: Click the collection name to redirect to the dataset page with the datasets belonging to the collection. Hover over this collection name to display the description of the collection.
  6. Collection URL: Click to copy the URL of the collection.

Datasets

Datasets

  1. Number of datasets: Displays the count of datasets (e.g., "5/20" indicates 5 datasets match the current filter out of 20 total).
  2. Search and filtering options: This section contains a search bar and a list of filter options.
  3. Collapse filtering panel: This is a toggle button to collapse the filtering panel.
  4. Dataset Header: Datasets can be sorted by each column name by clicking the column name. By default, datasets are sorted by the updated date.
  5. Expand Dataset Details: Click to expand the dataset details. When expanded, it shows the Dataset Metrics, including biological dimensions, total transcripts, gene count, and available layers. Dataset details
  6. Dataset Name: Click the dataset name to launch the dataset in CartoScope. Hover over the dataset name to see which collections it belongs to.
  7. Dataset URL: Click to copy the URL of the dataset.

Finding Datasets

The catalog provides powerful tools to filter and find datasets relevant to your research. You can narrow down or reorder the list of datasets using the search bar, filter chips, and sorting options.

  • Keyword Search: Type to match names, tissues, diseases, and platforms, organisms, and sources.
  • Filter:
    • Tissues/Diseases/Platforms/Organisms/Species/Sources/Collections: Click each expand button to show its filter options. Click on tags to filter by specific options. For example, click on platform tags (e.g., Visium HD, Xenium, Seq-Scope) to show only datasets generated by specific technologies.
    • N of Datasets: Filter the collection by the min and max number of datasets in the collection.
    • Date Range: Filter the collection by the start and end date of the datasets or collections.