import_segmentation (generic function)
import_segmentation_ij.Rd
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(s, mouse_ID = NA, channels = NULL)
# S3 method for mouse
import_segmentation_ij(
m,
slice_ID = NA,
hemisphere = NULL,
channels = NULL,
replace = FALSE
)
Arguments
- ...
- s
slice object
- 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.
- m
mouse object
- slice_ID
(str) ID of slice
- hemisphere
(str)'left', 'right' or NULL
- replace
(bool, default = FALSE) replace existing raw segmentation data
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
s <- import_segmentation(s, mouse_ID = "255") # Defaults to channels stored in slice attributes
#> Error in import_segmentation(s, mouse_ID = "255"): could not find function "import_segmentation"
s <- import_segmentation(s, mouse_ID = "255", channels = c("cfos", "eyfp", "colabel")) # Specify channels
#> Error in import_segmentation(s, mouse_ID = "255", channels = c("cfos", "eyfp", "colabel")): could not find function "import_segmentation"
m <- import_segmentation(m, slice_ID = "1_10", channels = c("cfos", "eyfp", "colabel"), replace = FALSE)
#> Error in import_segmentation(m, slice_ID = "1_10", channels = c("cfos", "eyfp", "colabel"), replace = FALSE): could not find function "import_segmentation"