make_segmentation_object (generic funciton)
make_segmentation_object.Rd
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(
s,
mouse_ID = NA,
channels = NULL,
use_filter = FALSE,
...
)
# S3 method for mouse
make_segmentation_object(
m,
slice_ID = NA,
hemisphere = NULL,
channels = NULL,
replace = FALSE,
use_filter = FALSE,
...
)
Arguments
- ...
(optional) additional volume and overlap parameters for get.colabeled.cells().
- s
slice object
- 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.
- m
mouse object
- slice_ID
(str) ID of slice
- hemisphere
(str, default = NULL) 'left', 'right' or NULL (both)
- replace
(bool, default = FALSE) replace existing raw segmentation data
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
s <- make_segmentation_object(s, mouse_ID = "255", channels = c("cfos", "eyfp"), use_filter = FALSE)
#> Error in make_segmentation_object(s, mouse_ID = "255", channels = c("cfos", "eyfp"), use_filter = FALSE): object 's' not found
m <- make_segmentation_object(m, slice_ID = '1_9', hemisphere = 'left', channels = c('eyfp', 'cfos', 'colabel'), use_filter = FALSE)
#> Error in make_segmentation_object(m, slice_ID = "1_9", hemisphere = "left", channels = c("eyfp", "cfos", "colabel"), use_filter = FALSE): object 'm' not found