get_pachytene: get_pachytene

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

Description

Identifies crops in pachytene

Usage

get_pachytene(
  img_path,
  species_num = 20,
  offset = 0.2,
  ecc_thresh = 0.85,
  area_thresh = 0.06,
  annotation = "off",
  channel2_string = "SYCP3",
  channel1_string = "MLH3",
  file_ext = "jpeg",
  KO_str = "--",
  WT_str = "++",
  KO_out = "-/-",
  WT_out = "+/+",
  path_out = img_path,
  artificial_amp_factor = 3,
  strand_amp = 2,
  resize_l = 120
)

Arguments

img_path,	path containing crops analyse
species_num,	number of chromosomes in the species
offset,	Pixel value offset used in therholding for the synaptonemal complex (SYCP3) channel
ecc_thresh,	The minimum average eccentricity of all objects in mask determined by computefeatures, for a cell to be pachytene.
area_thresh,	The minimum ratio of pixels included in mask to total, for a cell to be classified as pachytene.
annotation,	Choice to output pipeline choices (recommended to knit)
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. tiff jpeg or png.
KO_str	string in filename corresponding to knockout genotype. Defaults to –.
WT_str	string in filename corresponding to wildtype genotype. Defaults to ++.
KO_out	string in output csv in genotype column, for knockout. Defaults to -/-.
WT_out	string in output csv in genotype column, for knockout. Defaults to +/+.
path_out,	user specified output path. Defaults to img_path
artificial_amp_factor	Amplification of foci channel, for RGB output files. Deaults to 3.
strand_amp	multiplication of strand channel.
resize_l	length of resized square cell image.

Details

This function takes the crops make by auto_crop fast, and determines the number of synaptonemal complex candidates by considering the local background and using EBImage functions. In general, very bright objects which contrast highly with the background will be classified as the same object. Dim objects will likely be classified as many different objects. If the number of objects is too high compared to the species number (species_num) then the cell is determined to not be in pachytene. Note that this function has been optimized for mouse cells which can be very well spread / separated.

Value

Pairs of foci and synaptonemal channel crops for pachytene

Author(s)

Lucy McNeill

Examples

demo_path = paste0(system.file("extdata",package = "synapsis"))
SYCP3_stats <- get_pachytene(demo_path,ecc_thresh = 0.8, area_thresh = 0.04, annotation = "on")

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