What is Typical Background Layer Naming Scheme?¶
Background Layer Names: Names describing the source and type of the background visualization.
| Layer Name | Description |
|---|---|
| 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. |