make_segmentation_object (generic funciton) — make_segmentation

Make a wholebrain compatible segmentation object for a slice in a slice object

Make a wholebrain compatible segmentation object for a slice in a mouse object

Usage

make_segmentation_object(x, ...)

# S3 method for slice
make_segmentation_object(
  x,
  mouse_ID = NA,
  channels = NULL,
  use_filter = FALSE,
  ...
)

# S3 method for mouse
make_segmentation_object(
  x,
  slice_ID = NA,
  hemisphere = NULL,
  channels = NULL,
  replace = FALSE,
  use_filter = FALSE,
  ...
)

Arguments

x: a mouse or slice object
...: (optional) additional volume and overlap parameters for get.colabeled.cells().
mouse_ID: (str) ID of mouse
channels: (str vector, default = NULL) Channels to process. If NULL, defaults to the channels stored in the slice object attributes.
use_filter: (bool, default = FALSE). Use a filter to create more curated segmentation object from the raw segmentation data.
slice_ID: (str) ID of slice
hemisphere: (str, default = NULL) 'left', 'right' or NULL (both)
replace: (bool, default = FALSE) replace existing raw segmentation data

Value

a mouse or slice object

s slice object

Note

If you are processing the colabel channel, the X and Y positions of colabelled cells are the average of the x,y centroid coordinates of the colabelled objects

Examples

if (FALSE) {
s <- make_segmentation_object(s, mouse_ID = "255",
channels = c("cfos", "eyfp"), use_filter = FALSE)
}
if (FALSE) {
m <-  make_segmentation_object(m, slice_ID = '1_9', hemisphere = 'left',
channels = c('eyfp', 'cfos', 'colabel'), use_filter = FALSE)
}