isolate_dataset: Selectively isolate forward-warped cells *(W)*.

In jdknguyen/SMART: SMART (Semi-manual alignment to reference template): a pipeline for whole brain mapping projects

Selectively isolate forward-warped cells (W).

Description

Isolate a user-specified subset of the forward warped dataset. The user may use any or all of the available parameters they choose to isolate their cells of interest. An explanation of the isolate_dataset() parameters is provided below

Usage

isolate_dataset(
  setup,
  dataset,
  start_AP = NULL,
  end_AP = NULL,
  hemisphere = "B",
  plates = c(1:length(unique(dataset$image))),
  mirror = FALSE,
  flip = FALSE,
  bounds = c(),
  rois = c("grey")
)

Arguments

setup	(required) Setup list from setup_pl().
dataset	(required) Dataset output from forward_warp().
start_AP	(optional, default = NULL) Most anterior AP to retain cells.
end_AP	(optional, default = NULL) Most posterior AP to retain cells.
hemisphere	(optional, default = "B") Hemisphere to retain cells from ("L", "R", or "B").
plates	(optional, default = c(1:length(unique(dataset$image)))) Vector of registration plates to retain plates from; specify plate numbers relative to the first registration plate in the current analysis.
mirror	(optional, default = FALSE) Boolean to specify whether all cells will be mirrored across the midline.
flip	(optional, default = FALSE) Boolean to specify whether all cells will be flipped across the midline.
bounds	(optional, default = c()) Vector to specify whether cells within a circular or rectangular area should be retained. For circles, the vector should be formatted as: c("circle", ML-center, DV-center, radius). For rectangles, the vector should be formatted as: c("rectangle", ML-top-left-corner, DV-top-left-corner, width, height).
rois	(optional, default = c("grey")) Vector to specify regions of interest to retain cells from.

Value

Returns isolated_dataset a variable storing all cells retained from dataset.

jdknguyen/SMART documentation built on May 30, 2022, 10:51 p.m.