crop_single_object_fast {synapsis}R Documentation

crop_single_object_fast

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


[Package synapsis version 1.0.0 Index]