Normalize cell counts per mm^2^ or by mm^3^ (if multiplying by the stack size).
normalize_cell_counts.RdRun this function after all the slices that you want to process are finished being added
and you have combined your cell counts with get_cell_table(). This functions process all channels
where a cell table was made using the latter function.
Usage
normalize_cell_counts(
m,
combine_hemispheres = TRUE,
simplify_regions = TRUE,
simplify_keywords = c("layer", "part", "stratum", "division", "leaflet",
"Subgeniculate", "island", "Islands", "Fields of Forel", "Cajal", "Darkschewitsch",
"Precommissural"),
split_hipp_DV = TRUE,
DV_split_AP_thresh = -2.7
)Arguments
- m
mouse object
- combine_hemispheres
(bool, default = TRUE) Combine normalized cell counts from both hemispheres
- simplify_regions
(bool, default = TRUE ) simplify the normalized region counts based on keywords in the internal function,
simplify_keywords- simplify_keywords
(str vec, default = c("layer","part","stratum","division")). Keywords to search through region names and simplify to parent structure
- split_hipp_DV
(bool, default = TRUE) Split the subregions of the CA1, CA2, CA3, and DG based on a specified AP coordinate cutoff. This is because the Allen atlas doesn't have a dorsal/ventral region designation for these ROIs.
- DV_split_AP_thresh
(numeric, default = -2,7) The specified AP coordinate threshold to split hippocampal cell counts into dorsal and ventral.