clean_duplicates: Duplicate cell cleanup *(W)*

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

Description

Duplicate cell count clean up of segmentation output from the seg_loop() function. For use with mapping whole brain only. Note: if the imaging dataset is large this will be a time intensive process. Processing time will be printed once the function is finished.

Usage

clean_duplicates(
  setup,
  segs,
  xy_thresh = 1,
  z_thresh = 10,
  compare_depth = 200
)

Arguments

setup	(required) Contains setup parameters.
segs	(required) Segmentation data.
xy_thresh	(optional, default = 1) Threshold in the xy planes for the minimum distance where two center points can be the same cell.
z_thresh	(optional, default = 10) Threshold (in um) in the z-plane for the maximum z distance before a cell is counted as another cell.
compare_depth	(optional, default = 200) Comparision depth in (um). Compare a single image with adjacent images up to 200 um posterior.

Value

Returns the segmentation data in segs with clean cell output. All duplicate counts have been assigned NA.

mjin1812/SMART documentation built on Oct. 30, 2021, 7:25 p.m.