Function to transform coordinates for each mouse and extract layer boundary estimates

This function transforms the raw x,y coordinates of cells into laminar (y) and columnar (x) coordinates, bins the data, and estimates layer boundaries for each mouse in the dataset. It generates plots to visualize the transformation process and can optionally save these plots. This function was written for "in house" use by Michael Barkasi, and was not intended for general use. You can try it, but it may not work for your data and isn't documented in a user-friendly way.

Usage

cortical_coordinate_transform(
  count_data,
  total_bins,
  keep_plots = FALSE,
  L1_removed = TRUE,
  nat_left = FALSE,
  nat_right = FALSE,
  verbose = TRUE
)

Arguments

count_data: A list containing the count data and slice plots for each mouse, as produced by the make_count_data_h5 or make_count_data_csv functions
total_bins: Number of bins into which to divide the spatial axes, e.g., 100
keep_plots: Logical, whether to keep the generated plots in the output (default is FALSE)
L1_removed: Logical, whether the data in count_data has L1 removed (default is TRUE)
nat_left: Logical, setting used based on manual visual checks to ensure consistent orientation, causes angle and coordinate sign flips in layer leveling (default is FALSE)
nat_right: Logical, setting used based on manual visual checks to ensure consistent orientation, causes angle and coordinate sign flips in layer leveling (default is FALSE)
verbose: Logical, whether to print progress messages (default is TRUE)

Value

A list containing the transformed count data, layer boundary estimates, and optionally the generated plots