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How to Inspect

Inspection allows you to examine the detailed data associated with spots on the map, such as gene expression levels, factor probabilities, or cell identifiers.

1. Activate Inspector

Inspector

  1. Click the Inspect button in the Top Bar to toggle the Inspector tool.
  2. Choose an inspection mode:
    • Click Mode: Click a spot on the map to view comprehensive details in a persistent Inspector Drawer.
    • Hover Mode: Hover over a spot to see a quick summary in a pop-over tooltip.

2. Inspection Modes

Hover Mode (Tooltip)

Hover Mode

Provides a lightweight summary of the spot under your cursor.

  • Best for: Quick checks and exploring dense data.
  • Shows: Primary identifiers (ID/Cell ID), top factor, and key metrics.

Click Mode (Drawer)

Click Mode

Opens a dedicated side drawer with full details.

  • Best for: Deep analysis and copying data.
  • Shows: All available properties, full probability distributions, and raw values.

3. Data by Layer Type

The type of data shown depends on the layer you are inspecting.

Gene Layers

Displays gene expression counts at the inspected location.

  • Count / nUMI: The number of unique molecular identifiers found.
  • Gene Name: The specific gene identifier.

Factor Layers (Hex / Cells)

Displays the results of factor analysis for aggregated regions or segmented cells.

  • Top Factor: The factor with the highest probability for this spot.
  • Probability: The confidence score (0-100%) of the assignment.
  • Factor Distribution: A broken-down list of probabilities for all factors present at this location, sorted by likelihood.

Factor Layers (Raw Pixel)

For raw pixel layers, the inspector often shows combined information:

  • Gene Information: If available, the specific gene molecule at that pixel.
  • Factor Probabilities: The probability of this specific molecule belonging to various factors.

4. Navigating Multiple Items

At a single location (especially in pixel-based views), there may be multiple data points stacked (e.g., multiple gene molecules in one pixel).

  • Pagination: Use the Left and Right arrow keys on your keyboard or the on-screen arrows to step through each item individually.
  • Summary View: If there are many items, a summary list table may appear first, allowing you to see an overview before drilling down.

Keyboard Shortcuts

In both Hover and Click modes, you can use the Left and Right arrow keys to quickly cycle through overlapping features without moving your mouse.

FAQ