make_segmentation_filter (generic function)

Make a segmentation filter for a slice object

Make a segmentation filter for a slice within a mouse object

Usage

make_segmentation_filter(x, ...)

# S3 method for slice
make_segmentation_filter(
  s,
  channels = "eyfp",
  params = list(c("Vol..unit.", "Moment1", "Moment2", "Moment3", "Moment4", "Sigma")),
  ranges = list(list(c(200, 12000), c(3, 50), c(0, 600), c(0, 2000), c(0, 5), c(20,
    Inf)))
)

# S3 method for mouse
make_segmentation_filter(
  m,
  slice_ID = NA,
  hemisphere = NULL,
  channels = c("eyfp"),
  params = list(c("Vol..unit.", "Moment1", "Moment2", "Moment3", "Moment4", "Sigma")),
  ranges = list(list(c(200, 12000), c(3, 50), c(0, 600), c(0, 2000), c(0, 5), c(20,
    Inf))),
  replace = FALSE
)

Arguments

...
channels: (str vector, default = "eyfp") Channels to process. If NULL, defaults to the channels stored in the slice object attributes (not recommended).
params: (list) Has same length as channels. Each element contains a vector of parameters names used for filtering that channel
ranges: (list of lists) Has same length as channels. Each element of outer list corresponds the order of channels you want to process. Inner list contains vectors of parameter ranges for that channel.
m: mouse object
slice_ID: (str) ID of slice
hemisphere: 'left', 'right' or NULL (both)
replace: (bool, default = FALSE) replace existing filters.

Value

s slice object. Vector of indices of cells to remove are stored as the channel filters in the slice object.

m mouse object. Vector of indices of cells to remove are stored as the channel filters in the slice object within the mouse.

Examples

s <- make_segmentation_filter(s, channels = c('eyfp'),
params = list(c("Vol..unit.","Moment1","Moment2","Moment3","Moment4","Sigma")),
ranges = list(list(c(200, 12000), c(3, 50), c(0, 600), c(0, 2000), c(0, 5), c(20, Inf))))
#> Error in make_segmentation_filter(s, channels = c("eyfp"), params = list(c("Vol..unit.",     "Moment1", "Moment2", "Moment3", "Moment4", "Sigma")), ranges = list(list(c(200,     12000), c(3, 50), c(0, 600), c(0, 2000), c(0, 5), c(20, Inf)))): object 's' not found
m <- make_segmentation_filter(m, slice_ID = '1_10', hemisphere = NULL , channels = c('eyfp'),
params = list(c("Vol..unit.","Moment1","Moment2","Moment3","Moment4","Sigma")),
ranges = list(list(c(200, 12000), c(3, 50), c(0, 600), c(0, 2000), c(0, 5), c(20, Inf))))
#> Error in make_segmentation_filter(m, slice_ID = "1_10", hemisphere = NULL,     channels = c("eyfp"), params = list(c("Vol..unit.", "Moment1",         "Moment2", "Moment3", "Moment4", "Sigma")), ranges = list(list(c(200,         12000), c(3, 50), c(0, 600), c(0, 2000), c(0, 5), c(20,         Inf)))): object 'm' not found