BioFormatsImage: On disk representation of BioFormats images in SFE object

In pachterlab/SpatialFeatureExperiment: Integrating SpatialExperiment with Simple Features in sf

On disk representation of BioFormats images in SFE object

Description

'r lifecycle::badge("experimental")' At present, the BioFormatsImage is designed for OME-TIFF from Xenium and has not been tested on other formats that can be read with BioFormats. The image is not loaded into memory, and when it is, the the BioFormatsImage object is converted into ExtImage because the loaded image is of a class that inherits from Image. The ExtImage class is a thin wrapper inheriting from VirtualSpatialImage so it's compatible with SpatialExperiment from which SFE is derived. This class might drastically change as it matures, say to accommodate other formats supported by BioFormats and to store the transformation matrix rather than loading image into memory upon transform.

Usage

## S4 method for signature 'BioFormatsImage'
show(object)

BioFormatsImage(
  path,
  ext = NULL,
  isFull = TRUE,
  origin = c(0, 0),
  transformation = list()
)

Arguments

object	A BioFormatsImage object.
path	Path to an OME-TIFF image file.
ext	Numeric vector with names "xmin", "xmax", "ymin", "ymax" in microns indicating the spatial extent covered by the image. If NULL, then the extent will be inferred from the metadata, from physical pixel size and the number of pixels.
isFull	Logical, if the extent specified in ext is the full extent. If ext = NULL so it will be inferred from metadata then isFull = TRUE will be set internally.
origin	Origin of the whole image in the x-y plane, defaults to c(0,0). This is shifted when the image is translated. This is not the same as xmin and xmax. For example, when the extent is only part of the whole image and the whole image itself can be spatially translated, the origin is needed to determine which part of the whole image this extent corresponds to.
transformation	Named list specifying affine transformation. The list can have names "name" and named parameter of the transformation, e.g. list(name = "mirror", direction = "vertical"), "rotate" and degrees = 90 (clockwise), and "scale" and factor = 2. The list can also have names "M" for a 2x2 linear transformation matrix in the xy plane and "v" for a translation vector of length 2 to specify general affine transformation.

Details

Spatial extent is inferred from OME-TIFF metadata if not specified. Physical pixel size from the metadata is used to make the extent in micron space. If physical pixel size is absent from metadata, then the extent will be in pixel space, which might mean that the image will not align with the geometries because often the geometry coordinates are in microns, so a warning is issued in this case.

Affine transformations can be specified in the transformation argument, either by name or by directly specifying the matrix. The transformations specified by name will always preserve the center of the image. When named transformations are chained, name and parameter will be converted to matrix and translation vector the second time a transformation is specified. If the subsequent transformation happens to restore the image to its original place, then transformation specifications will be removed.

Value

A BioFormatsImage object.

See Also

[isFull()], [origin()]

pachterlab/SpatialFeatureExperiment documentation built on May 17, 2024, 12:24 a.m.