R/SMART.R

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

#' SMART (Semi-manual alignment to reference template): a pipeline for whole brain mapping projects.
#'
#' @description
#' This package interfaces with the [wholebrain] package by Daniel Furth to process
#' whole brain imaging datasets. The pipeline is split into five different
#' parts, with the purpose of each function per part explained below. Note that
#' all functions that are exclusively meant to be used with whole brain datasets
#' will be marked with a **(W)** next to the function. Unmarked functions can be
#' used on single slice datasets across the brain.
#'
#' @details For convention, if a return value is given by a function,
#' the recommended variable name is indicated in italics in the return
#' section of each function's help page. If this return value is a
#' required argument for another function in the pipeline, the
#' the recommended variable name will also be the same name as the argument.
#'
#' @section Part 1. Setup pipeline:
#'
#' 1) [setup_pl()] User friendly way to setup parameters for whole or
#' partial brain pipeline analysis.
#' 2) [im_sort()]  A function to sort image paths for imaging datasets.
#' 3) [get_savepaths()] Generate savepaths and save directories.
#'
#' @section Part 2. Alignment (whole brain dataset):
#'
#' 1) [choice()] **(W)** User friendly choice game to align internal
#'    reference atlas plates.
#' 2) [brainmorph()] **(W)** Generate a brain morph plot.
#' 3) [interpolate()] **(W)** Interpolate all AP and z numbers
#'    for atlas plates in a whole brain project
#'
#' @section Part 3. Registration:
#'
#' 1) [registration2()] Console user interface built on top of
#' registration() function from the wholebrain package.
#' 2) [regi_loop()] Automatically loops through the image registration
#' processs for the imaging dataset.
#'
#' @section Part 4. Segmentation and forward warping:
#'
#' 1) [filter_loop()] Loops through reference slices and allows user to
#' check/change filter settings for segmentation or registration throughout the
#' brain.
#' 2) [seg_loop()] Loop through and segment images in the segmentation channel.
#' 3) [clean_duplicates()] **(W)** Duplicate cell count clean up of segmentation
#' output
#' 4) [forward_warp()] Perform forward warp loop back onto atlas space using
#' segmentation and registration data.
#'
#' @section Part 5. Dataset manipulation and plotting:
#'
#' 1) [get_rois()] Get subset of the forward warped dataframe of just regions of
#' interest.
#' 2) [get_sunburst()] Generate a sunburst plot using a forward warped dataset.
#' 3) [get_tree()] Create a dataframe of hierarchical region cell count data.
#' 4) [glassbrain2()] Generate 3D plot of cells with option of plotting or
#' removing glassbrain in the background.
#' 5) [get_table()] Generates a dataframe showing region acronyms, their full
#' name, hierachical paths, total cell counts, left and right counts, and cell
#' count percentages.
#' @md
#' @docType package
#' @name SMART
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