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Typical Layer Naming Scheme

It is helpful to recognize common naming conventions for layers you might encounter or create in CartoScope.

Background Layers

  • 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.

Factor Layers

  • 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.