get_blobs: get_blobs

In mcneilllucy/synapsis: An R package to automate the analysis of double-strand break repair during meiosis

Description

Makes mask of all objects bright enough to be classified as a cell cadidate

Usage

get_blobs(
  img_orig,
  blob_factor,
  bg_blob_factor,
  offset,
  final_blob_amp,
  brush_size_blob,
  sigma_blob,
  watershed_tol,
  watershed_radius,
  crowded_cells,
  annotation
)

Arguments

img_orig	Original image
blob_factor,	Contrast factor to multiply original image by before smoothing/smudging
bg_blob_factor,	Contrast factor to multiply original image by to take background. Used prior to thresholding.
offset,	Pixel value offset from bg_blob_factor. Used in thresholding to make blob mask.
final_blob_amp,	Contrast factor to multiply smoothed/smudged image. Used in thresholding to make blob mask.
brush_size_blob,	Brush size for smudging the synaptonemal complex channel to make blobs
sigma_blob,	Sigma in Gaussian brush for smudging the synaptonemal complex channel to make blobs
watershed_tol	Intensity tolerance for watershed method. Defaults to 0.05.
watershed_radius	Radius (ext variable) in watershed method used in strand channel. Defaults to 1 (small)
crowded_cells	TRUE or FALSE, defaults to FALSE. Set to TRUE if you have many cells in a frame that almost touch
annotation,	Choice to output pipeline choices (recommended to knit) have many cells in a frame that almost touch

Value

Mask with cell candidates

mcneilllucy/synapsis documentation built on Dec. 21, 2021, 3:59 p.m.