Skip to content

Layer Drawer

The Layer Drawer is the central hub for managing all visualization layers in CartoScope. It is located on the left side of the screen and can be toggled using the Layer Icon in the top bar.

Functionality

  • Layer List: Displays all currently loaded layers.
  • Reordering: Drag and drop layers to change their rendering order.
  • Layer Controller: Rename layers and adjust settings such as visibility, opacity, color, and scale.

Layer Groups

CartoScope categorizes layers into 4 groups:

  • Background (BG): Histology images or base maps.
  • Gene: Spatial plots of individual gene expression.
  • Factor: Result layers from spatial factor analysis (e.g., FICTURE).
  • ROI: Region of Interest layers containing user-defined shapes.

Typical Layer Naming Scheme

Common background layer names include:

  • Spatial gene expression density map: Spatial gene expression density map in black-white color scheme.
  • H&E histology staining: A brightfield histology image stained with hematoxylin (nuclei, purple/blue) and eosin (cytoplasm/extracellular matrix, pink) to reveal tissue structure and morphology.
  • DAPI nuclear staining: A fluorescence microscopy image where the DNA-binding dye DAPI labels cell nuclei, making them appear bright blue and allowing you to assess nuclear distribution, density, and morphology.
  • DAPI nuclear staining (maximum intensity projection): A 2D projection of the DAPI fluorescence across a z-stack, where each pixel shows the maximum nuclear signal to enhance visibility of nuclei throughout the volume.
  • Interior RNA staining: A staining layer highlighting intracellular RNA signal within cells, useful for evaluating overall RNA content and cytoplasmic signal distribution.
  • 18S rRNA staining: A staining layer marking 18S ribosomal RNA, often used as a strong, widespread RNA marker to assess RNA abundance and tissue/cell integrity.
  • Interior protein staining: A staining layer highlighting intracellular protein signal, useful for visualizing protein abundance and subcellular distribution within cells.
  • Cell boundary staining: A staining layer that outlines cell membranes/boundaries to support cell segmentation and interpretation of cell shape and organization.

Common factor layer names include:

  • FICTURE - N factor LDA with Wµm hexagons: FICTURE results layer, where N is the number of factors, and W is the hexagon bin size.
  • cell: Xenium cell segmentation (Xenium Ranger): Cell segmentation-based results layer from Xenium Ranger. This usually applies to the datasets from 10X Xenium.
  • cell: Visium HD cell segmentation (Space Ranger): Cell segmentation-based results layer from Space Ranger. This usually applies to the datasets from 10X Visium HD.
  • sqW: Visium HD WxWµm square bins (Space Ranger): Square bin-based results layer from Space Ranger, where W is the bin size. This usually applies to the datasets from 10X Visium HD.

Interface

Layer Drawer

1. Load Layers Button

Click to choose one layer type to load. This will open a dialog to select the layer file.

2. Layer List

The list displays all currently loaded layers, including the active layers and the hidden layers.

Components within the layer list

The following example shows four layers from top to bottom: a ROI layer, a gene layer, a factor layer, and a background layer.

Layer List

1) Layer Information fields

  • Layer Group: The category of the layer ("ROI", "Gene", "Factor", or "BG").
  • Color: The representative color (applies to Gene and ROI layers).
  • Layer Name: The display name of the layer. In the example, "#63617", "Apoe", "t18-f48...", and "H&E histology staining" identify an ROI, a gene, a factor result, and a background image, respectively.

2) Control fields

  • Delete Button: Remove the layer from the session.
  • Settings Button: Open the configuration panel for the layer:
    • Color: Set a specific color or assign a random one.
    • Opacity: Adjust the layer transparency.
    • Order: Move the layer to the front or back.
    • Visibility: Toggle the Eye Icon to show/hide the layer without deleting it.
    • Move Up/Down: Change the layer's position in the rendering stack.

3) (Factor Layer Only) Factor Layer Type

The type of the factor layer.

4) (Factor Layer Only) Factor View Button

Click to open the factor view drawer for this factor layer or display the information of this factor layer in the opened factor view drawer.

5) (Background Layer Only) Scale Button

Scales the background layer to fit the current viewport.

3. Map View Summary

The map view summary includes the zoom level, and the min and max X and Y coordinates of the current view.