clean_duplicates: Duplicate cell cleanup *(W)*

Description Usage Arguments Value

View source: R/clean_duplicates.R

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

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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 Aug. 8, 2019, 12:31 p.m.