The Staffli Class

The Staffli object is designed to hold information about the spatial data generated in a 10x Visium SRT experiment. This includes paths to images, spot coordinates as well as loaded images in raster format and additional information about these images.

Slots

imgs

A character vector of paths to the raw HE images

rasterlists

A list of lists containing images in 'raster' format

meta_data

A tibble with spot coordinates and additional meta data

image_height

The height of the scaled images in pixels

image_info

A tibble with information about the raw images

scalefactors

A tibble with information about scalefactors used to convert coordinates between the original image and down-scaled representations such as "tissue_lowres_image.jpg"

pixels_per_um

Numeric vector specifying the number of pixels in the raw images that corresponds to 1 micrometer

version

Package version.

Author

Ludvig Larsson