fsbrain (version 0.5.5)

vol.merge: Merge background volume and overlay to new colors.

Description

Merge background volume and overlay to new colors.

Usage

vol.merge(
  volume,
  overlay_colors,
  bbox_threshold = 0L,
  forced_overlay_color = NULL
)

Value

3D array of color strings, the merged colors

Arguments

volume

3D array, can be numeric (gray-scale intensity values) or color strings. If numeric, the intensity values must be in range `[0, 1]`.

overlay_colors

3D array of color strings, values which are not part of the overlay (and should display background in the result) must have `NA` instead of a color string. Must have same dimensions as the `volume`.

bbox_threshold

numerical, the threshold intensity used to separate background and foreground. All voxels with intensity values greater than this value in the background `volume` will be considered `foreground` voxels. Background-only slices at the borders of the volume will be discarded (in the merged, final image). Pass `NULL` to use the full image without applying any bounding box.

forced_overlay_color

NULL or an rgb color string, like '#FF0000' for red. If NULL, the activation colors will be used as foreground colors. Otherwise, the given color will be for all foreground vertices.

See Also

Other volume utility: vol.boundary.box(), vol.imagestack(), vol.overlay.colors.from.activation(), vol.planes(), vol.slice()