cellCounter: cell counter

In jianhong/cellCounter: cell counter

cell counter

Description

count the cells from a z-stack tiff or czi file and output xml for imageJ

Usage

cellCounter(
  file,
  channel = "green",
  offset = 0.05,
  cellSizeRange = c(20, 1000),
  distanceSameCell = 10,
  xmlfile = sub("\\.(tiff|tif)$", ".cellCounter.xml", file, ignore.case = TRUE),
  imageFilename = sub("\\.(tiff|tif)$", ".czi", basename(file), ignore.case = TRUE),
  counterType = c(prenew = 5, new = 4, old = 6),
  zvalue = fixZvalue,
  adjustPipeline = c(GaussianBlur, ScurveAdjust),
  detectFun = detectObjects,
  saveAdjustImage = NULL,
  silence = FALSE,
  ...
)

Arguments

file	tiff file name
channel	channel to be detected
offset	the offset of color from background, (0, 1).
cellSizeRange	cell size range
distanceSameCell	distance of same cell in different frame
xmlfile	filename of xml
imageFilename	filename of the original czi file
counterType	counterType in Cell Counter of imageJ
zvalue	change the z to original z.
adjustPipeline	adjust pipeline before cell detection
detectFun	the function used to detect the cell, see detectObjects, detectObjects2.
saveAdjustImage	the file name for adjusted image. NULL to ignore saving.
silence	output the message or not
...	parameters could be used in the pipeline

Author(s)

Jianhong Ou

Examples

library(EBImage)
library(scales)
library(XML)
##library(rJava)
##.jinit(parameters=c("-Xms1g","-Xmx4g"))
##library(RBioFormats) ## to support czi file,
## try to install by devtools::install_github("aoles/RBioFormats")
cellCounter(system.file("extdata", "sample.tiff", package="cellCounter"),
xmlfile="sample.xml", imageFilename="sample.czi")

jianhong/cellCounter documentation built on June 10, 2022, 8 p.m.