Description Details Part 1. Setup pipeline Part 2. Alignment (whole brain dataset) Part 3. Registration Part 4. Segmentation and forward warping Part 5. Dataset manipulation and plotting
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.
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.
setup_pl()
User friendly way to setup parameters for whole or
partial brain pipeline analysis.
im_sort()
A function to sort image paths for imaging datasets.
get_savepaths()
Generate savepaths and save directories.
choice()
(W) User friendly choice game to align internal
reference atlas plates.
brainmorph()
(W) Generate a brain morph plot.
interpolate()
(W) Interpolate all AP and z numbers
for atlas plates in a whole brain project
registration2()
Console user interface built on top of
registration() function from the wholebrain package.
regi_loop()
Automatically loops through the image registration
processs for the imaging dataset.
filter_loop()
Loops through reference slices and allows user to
check/change filter settings for segmentation or registration throughout the
brain.
seg_loop()
Loop through and segment images in the segmentation channel.
clean_duplicates()
(W) Duplicate cell count clean up of segmentation
output
forward_warp()
Perform forward warp loop back onto atlas space using
segmentation and registration data.
get_rois()
Get subset of the forward warped dataframe of just regions of
interest.
get_sunburst()
Generate a sunburst plot using a forward warped dataset.
get_tree()
Create a dataframe of hierarchical region cell count data.
glassbrain2()
Generate 3D plot of cells with option of plotting or
removing glassbrain in the background.
get_table()
Generates a dataframe showing region acronyms, their full
name, hierachical paths, total cell counts, left and right counts, and cell
count percentages.
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