cellCounterSingleFrame: cell counter

In jianhong/cellCounter: cell counter

cell counter

Description

count the cells from a single frame tiff file and output xml for imageJ

Usage

cellCounterSingleFrame(
  file,
  channels = c("red", "green", "blue"),
  formula,
  maskValue = 0.3,
  offset = 0.1,
  cellSizeRange = c(10, 1000),
  xmlfile = sub("\\.(tiff|tif)$", ".cellCounter.xml", file, ignore.case = TRUE),
  imageFilename = sub("\\.(tiff|tif)$", ".czi", basename(file), ignore.case = TRUE),
  adjustPipeline = c(ScurveAdjust),
  detectFun = detectObjects,
  saveAdjustImage = NULL,
  silence = FALSE,
  ...
)

Arguments

file	tiff file name
channels	channel to be detected
formula	the relationship of channels. Here '*'=='intersect' and '+'=='contain' eg. blue*green+red means the cell must have blue and green, and red is in the cell. blue*green-red means the cell must have blue and green, and red is NOT in the cell. blue*green means the cell must have blue and green blue+red means the cell must have blue, and red is in the cell.
maskValue	the cutoff value for set the mask is TRUE.
offset	the offset of color from background, (0, 1).
cellSizeRange	cell size range
xmlfile	filename of xml
imageFilename	filename of the original czi file
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 saveing.
silence	output the message or not
...	parameters could be used in the pipeline

Author(s)

Jianhong Ou

Examples

library(EBImage)
library(scales)
library(XML)
cellCounterSingleFrame(system.file("extdata", "low.jpg", package="cellCounter"), 
formula="blue+red", xmlfile="low.xml", imageFilename="low.jpg")

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