SpatialImage-class {SpatialExperiment} | R Documentation

## The SpatialImage class

### Description

The `SpatialImage` class hierarchy provides representations of images from a variety of sources. It is used by the SpatialExperiment class to manage the loading of images across multiple studies.

### Constructor

`SpatialImage(x, is.url)` will return a SpatialImage object. The class of the object depends on the type of `x`:

- If `x` is a raster object, a LoadedSpatialImage is returned. This represents an image that is fully realized into memory, where the raster representation is stored inside the output object.

- If `x` is a string and `is.url=TRUE` or it starts with `"http://"`, `"http://"` or `"ftp://"`, a RemoteSpatialImage is returned. This represents an image that is remotely hosted and retrieved only on request.

- If `x` is a string and `is.url=TRUE` or it does not start with a URL-like prefix, a StoredSpatialImage is returned. This represents an image that is stored in a local file and is loaded into memory only on request.

### Getting the raster image

For a SpatialImage object `x`, `imgRaster(x, ...)` will return a raster object (see `?as.raster`). This is effectively a matrix of RGB colors for each pixel in the image.

For a StoredSpatialImage object `x`, additional arguments in `...` are passed to `image_read`. This controls how the image is read into memory.

For a RemoteSpatialImage object `x`, the image file is first downloaded before the raster is returned. Here, `...` may contain an extra `cache` argument, which should be a BiocFileCache object (from the BiocFileCache package) specifying the file cache location. The default location is determined by `options("SpatialExperiment.remote.cache.path")`, otherwise it defaults to a subdirectory in the R temporary directory. Any further named arguments in `...` are passed to `image_read`.

`as.raster(x, ...)` is the same as `imgRaster(x, ...)`.

### In-memory caching

For StoredSpatialImage and RemoteSpatialImage objects, loading the image with `imgRaster` will automatically store the loaded raster object in an in-memory cache. Any subsequent `imgRaster` call will retrieve the raster from the cache, avoiding costly retrieval from the file system.

The cache policy is to evict the least recently used images when a new image would be added that exceeds the maximum cache size. If the new image by itself exceeds the maximum cache size, all images are evicted from the cache to trigger garbage collection and free up memory.

By default, the maximum size of the cache is 4 GB. This can be modified by setting `options("SpatialExperiment.cache.size")` to some number of bytes, e.g., `2^32`.

### Other methods

`dim(x)` will return an integer vector of length 2, containing the width and height of the image in pixels. Note that this calls `imgRaster` under the hood and thus may interact with the file and memory caches as described above.

For any SpatialImage `x`, `as(x, "LoadedSpatialImage")` will create a LoadedSpatialImage containing an in-memory raster object.

For a RemoteSpatialImage `x`, `as(x, "StoredSpatialImage")` will create a StoredSpatialImage pointing to the file cache location.

### Author(s)

Aaron Lun

### Examples

    path <- system.file(
      "extdata", "10xVisium", "section1", "spatial",
      "tissue_lowres_image.png", package="SpatialExperiment")

    spi <- SpatialImage(path)
    plot(imgRaster(spi))

    # the following operations all use the cache
    # so there is no need to reload the image
    nrow(spi)
    ncol(spi)
    plot(as.raster(spi))

    # coercing to an explicitly in-memory raster
    spi <- as(spi, "LoadedSpatialImage")
    plot(as.raster(spi))

[Package SpatialExperiment version 1.4.0 Index]