get.buds: Import and normalize ImageJ ROIs to cell coordinates

In maekiniemi/yeastTracker:

Description

This function loads ImageJ roi zip files. It returns a list object with rois normalized into coordinate system as well as mother/bud relations.

Usage

get.buds(
  x,
  THRESHOLD = 80,
  borderCol = rgb(0, 0, 0, 0.2),
  fillCol = NA,
  add = FALSE,
  xlab = "",
  ylab = "",
  main = "get buds",
  asp = 1,
  ...
)

Arguments

x	.roi object from read.ijzip().
THRESHOLD	an integer value specifying the area in pixels needed for an overlap to count as mother/budded relation. Default value is 100.
borderCol	color value for overlap boundary.
add	plot in the same coordinate system. default FALSE
xlab	x axis label. Default empty.
ylab	y axis label. Default empty.
main	header. Default "get buds"
asp	set the aspect ratio of the plot. Default 1.
fillcol	color value for overlap filling

Examples

filename<-system.file('data/YET629_02_w1L488nm-L561nm_sequence-10000.zip', package='yeast')
roi <- read.ijzip(filename)
yeastCells<-get.buds(roi)

maekiniemi/yeastTracker documentation built on June 9, 2020, 1:40 p.m.