Detect atlas regions that only show up in a single slice object within a mouse.

Quality check function to make sure that the regions included for analysis show up in more than 1 slice object, otherwise the user can remove exceptions from the mouse object.

Regions counts derived from only one image may be less accurate. This function can generate a log of these regions so the user can qualitatively evaluate the raw data. Users also have to option of removing these regions automatically from normalized_counts dataframe.

The user should run normalize_cell_counts() and get_cell_table() functions prior to using this function.

Usage

detect_single_slice_regions(m, remove = FALSE, log = TRUE)

Arguments

m

mouse object

remove

(bool, FALSE) Remove any regions in the normalized counts table that

log

(bool, TRUE) Save the regions that don't have enough n into a .csv file in the output folder.

Value

mouse object