import_segmentation (generic function) — import_segmentation

Method for importing segmentation data for a slice object

Method for importing segmentation data for a mouse object

Usage

import_segmentation_ij(x, ...)

# S3 method for slice
import_segmentation_ij(x, mouse_ID = NA, channels = NULL, maxdist = 10, ...)

# S3 method for mouse
import_segmentation_ij(
  x,
  slice_ID = NA,
  hemisphere = NULL,
  channels = NULL,
  maxdist = 10,
  replace = FALSE,
  ...
)

Arguments

x: a mouse or slice object
...: further arguments passed to or from other methods.
mouse_ID: (str) ID of mouse
channels: (str vector, default = NULL) channels to import. If NULL, defaults to the channels stored in the slice object attributes.
maxdist: (int, default = 10) maximum tolerability of character differences to match the string names of the importation files
slice_ID: (str) ID of slice
hemisphere: (str)'left', 'right' or NULL
replace: (bool, default = FALSE) replace existing raw segmentation data

Value

a mouse or slice object

s slice object

m mouse object

Note

The designated colabel channel name in this pipeline will auto import the output of the batch_3D_MultiColocalization.ijm macro provided in the pre-processing pipeline. If you have a separate method used for detecting colabelled cells, please use a different naming convention for this channel, e.g. "colabel_PV_cfos", and import using a customized import function such as import_segmentation_custom().

Examples

if (FALSE) {
s <-  import_segmentation(s, mouse_ID = "255")
s <-  import_segmentation(s, mouse_ID = "255",
channels = c("cfos", "eyfp", "colabel"))
}
if (FALSE) {
m <-  import_segmentation(m, slice_ID = "1_10",
channels = c("cfos", "eyfp", "colabel"), replace = FALSE)
}