forward_warp: Forward warp back to atlas space

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

Forward warp back to atlas space

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().

sgoldenlab/SMART documentation built on March 20, 2022, 5:16 p.m.