crop_single_object_fast: crop_single_object_fast

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

Description

Creates mask for every individual cell candidate in mask

Usage

crop_single_object_fast(
  retained,
  OOI_final,
  counter_final,
  img_orig,
  img_orig_foci,
  img_orig_DAPI = "blank",
  file_sc,
  file_foci,
  file_DAPI = "blank",
  cell_count,
  mean_pix,
  annotation,
  file_base,
  img_path,
  r_max,
  cx,
  cy,
  channel3_string,
  channel2_string,
  channel1_string,
  file_ext,
  third_channel,
  path_out,
  img_orig_highres,
  resize_l,
  crowded_cells,
  cropping_factor
)

Arguments

retained	Mask of cell candidates which meet size criteria. After smoothing/smudging and thresholding.
OOI_final,	Objects of interest count. Total number of cell candidates in retained.
counter_final,	Counter for single cell we are focussing on. Remove all other cells where counter_single not equal to counter_final.
img_orig,	description
img_orig_foci,	description
img_orig_DAPI,	description
file_sc,	filename of synaptonemal complex channel image
file_foci,	filename of foci channel image
file_DAPI,	filename of DAPI channel image
cell_count,	counter for successful crops around cells
mean_pix,	Mean pixel intensity of cell crop (in SYCP3 channel) for normalisation
annotation,	Choice to output pipeline choices (recommended to knit)
file_base,	filename base common to all three channels i.e. without -MLH3.jpeg etc.
img_path,	path containing image data to analyse
r_max	maximum radius of blob for cropping
cx	centre of blob x
cy	centre of blob y
channel3_string	Optional. String appended to the files showing the channel illuminating cell structures. Defaults to DAPI, if third channel == "on".
channel2_string	String appended to the files showing the channel illuminating synaptonemal complexes. Defaults to SYCP3
channel1_string	String appended to the files showing the channel illuminating foci. Defaults to MLH3
file_ext	file extension of your images e.g. tif jpeg or png.
third_channel	Optional, defaults to "off". Set to "on" if you would also like crops of the third channel.
path_out,	user specified output path. Defaults to img_path
img_orig_highres	the original strand image with original resolution
resize_l	length of square to resize original image to.
crowded_cells	TRUE or FALSE, defaults to FALSE. Set to TRUE if you have many cells in a frame that almost touch
cropping_factor	size of cropping window square, as factor of characteristic blob radius. Defaults to 1. May need to increase if using watershed.

Value

Crops around all candidates in both channels

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