Read/Write calibrated 3D blocks of image data

Read/Write calibrated 3D blocks of image data

read.im3d(
  file,
  ReadData = TRUE,
  SimplifyAttributes = FALSE,
  ReadByteAsRaw = FALSE,
  ...
)

write.im3d(x, file, format = NULL, ...)

Arguments

file

Character vector describing a single file

ReadData

Whether to read the data itself or return metadata only. Default: TRUE

SimplifyAttributes

When TRUE leave only core im3d attributes.

ReadByteAsRaw

Whether to read byte values as R raw arrays. These occupy 1/4 memory but arithmetic is less convenient. (default: FALSE)

...

Arguments passed to methods

x

The image data to write (an im3d, or capable of being interpreted as such)

format

Character vector specifying an image format (e.g. "nrrd", "amiramesh"). Optional, since the format will normally be inferred from the file extension. See getformatwriter for details.

Value

For read.im3d an objecting inheriting from base array and im3d classes.

Details

Currently only nrrd and amira formats are implemented. Furthermore implementing a registry to allow extension to arbitrary formats remains a TODO item.

The core attributes of an im3d object are BoundingBox, origin, x, y , z where x, y, z are the locations of samples in the x, y and z image axes (which are assumed to be orthogonal).

See also

read.nrrd, read.amiramesh

write.nrrd, getformatwriter

Other im3d: as.im3d(), boundingbox(), im3d-coords, im3d(), imexpand.grid(), imslice(), is.im3d(), mask(), origin(), projection(), threshold(), unmask(), voxdims()

Examples

if (FALSE) {
# read attributes of vaa3d raw file
read.im3d("L1DS1_crop_straight.raw", ReadData = F, chan=2)
}