Method to plot spatially calibrated image arrays

# S3 method for im3d
  xlim = NULL,
  ylim = NULL,
  zlim = NULL,
  plotdims = NULL,
  flipdims = "y",
  filled.contour = FALSE,
  asp = 1,
  axes = FALSE,
  xlab = NULL,
  ylab = NULL,
  nlevels = 20,
  levels = pretty(zlim, nlevels + 1),
  color.palette = colorRampPalette(c("navy", "cyan", "yellow", "red")),
  col = color.palette(length(levels) - 1),
  useRaster = NULL,



The im3d object containing the data to be plotted (NAs are allowed).

xlim, ylim

ranges for the plotted x and y values, defaulting to the BoundingBox of x.


the minimum and maximum z values for which colors should be plotted, defaulting to the range of the finite values of z. Each of the given colors will be used to color an equispaced interval of this range. The midpoints of the intervals cover the range, so that values just outside the range will be plotted.


Which dimensions of 3D im3d object to plot (character vector). Defaults to c('x','y')


Which dimensions to flip (character vector). Defaults to flipping y.


Whether to use a filled.contour plot instead of a regular image plot.


Whether to have a a square aspect ratio (logical, default: FALSE)


Whether to plot axes (default: FALSE)

xlab, ylab

each a character string giving the labels for the x and y axis. Default to the ‘call names’ of x or y, or to "" if these were unspecified.


The number of colour levels in z


The levels at which to break z values


The colour palette from which col will be selected.


a list of colors such as that generated by rainbow, heat.colors, topo.colors, terrain.colors or similar functions.


Whether to use rasterImage to plot images as a bitmap (much faster for large images). default useRaster=NULL checks dev.capabilities to see if raster images are supported.


graphical parameters for plot or image may also be passed as arguments to this function.


A list with elements:

  • zlim The z (intensity limits)

  • nlevels.actual The actual number of plotted levels

  • nlevels.orig The requested number of plotted levels

  • levels The chosen levels

  • colors A character vector of colours


if (FALSE) { LHMask=read.im3d(system.file('tests/testthat/testdata/nrrd/LHMask.nrrd',package='nat')) image(imslice(LHMask,10), asp=TRUE) # useRaster is appreciably quicker in most cases image(imslice(LHMask,10), asp=TRUE, useRaster=TRUE) }