forward_warp: Forward warp back to atlas space

In mjin1812/SMART: SMART (Semi-manual alignment to reference template): a pipeline for whole brain mapping projects

Description

Loop through all segmented cells and perform forward warp loop back onto atlas space using registration and segmentation data. Options for plotting a schematic plot and saving forward warp images. For a whole brain, this function should be used after the segmentation list segs has been cleaned of duplicate cell counts. Note: if the imaging dataset is large this will be a time intensive process. Processing time will be printed once the function is finished.

Usage

forward_warp(
  setup,
  segs,
  regis,
  filetype = c("tif", "tiff", "wmf", "emf", "png", "jpg", "jpeg", "bmp", "ps", "eps",
    "pdf"),
  savewarp = TRUE,
  saveschematic = TRUE,
  plane = "coronal",
  title = FALSE,
  mm.grid = TRUE,
  dev.size = c(5.4, 4.465),
  pch = 21,
  cex = 0.5,
  col = "black",
  scale.bar = FALSE,
  region.colors = TRUE
)

Arguments

setup	(required) Setup list from setup_pl().
segs	(required) Segmentation data.
regis	(required) Registration data.
filetype	(optional, default = "tif") Image type to save as. See the type argument in the function savePlot(). Options: "tif", "tiff", "wmf", "emf", "png", "jpg", "jpeg", "bmp","ps", "eps", "pdf"
savewarp	(optional, default = TRUE) Save forward warp plot image in folder 'setup$savepaths$out_segmentation_warps'.
saveschematic	(optional, default = TRUE) Save schematic plot images in folder 'setup$savepaths$out_segmentation_schem'.
plane	(optional, default = "coronal") Atlas plane to register to. options: "coronal", "sagittal"
title	(optional, default = FALSE) Title for the schematic plot.
mm.grid	(optional, default = TRUE) Plot grid in schematic plot.
dev.size	(optional, default = c(5.4, 4.465)). See same argument from wholebrain::schematic.plot().
pch	(optional, default = 21) Graphical parameter for point shape.
cex	(optional, default = 0.5) Graphical parameter for text size.
col	(optional, default = "black") Graphical parameter for color.
scale.bar	(optional, default = TRUE) Display a measure bar in the schematic plot
region.colors	(optional, default = TRUE) Display Allen Brain Atlas colors in schemetic plot.

Value

Returns dataset a variable storing all mapped segmentation data to registration data.

See Also

See also wholebrain::schematic.plot().

mjin1812/SMART documentation built on Oct. 30, 2021, 7:25 p.m.