GetCELL: Cell Image Query

Description Usage Arguments Value Author(s) Examples

View source: R/GetCELL.R

Description

Return the combined image of given plate location and mark cell coordinates with a white circle

Usage

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GetCELL(SERVER = "MDCStore", ID = "moldev", PWD = "moldev", PlateID,
  WellID, SiteID = c(1, 1), Range = lapply(1:3, function(x) c(0, 0.1)),
  use.autoRange = T, col.order = c("blue", "green", "red"),
  channel.choice = 1:3, disp = "raster", TimeCourse = F,
  TimePoint = 1, returnMat = F, CellStep = 50, xcoord, ycoord,
  fullIm = T, ...)

Arguments

SERVER

the odbc connexion to MDCStore database. Ignored if DB given

ID

the identifiant for connexion. Ignored if DB given

PWD

the password for connexion. Ignored if DB given

PlateID

the PlateID of the image

WellID

the WellID of the image

SiteID

the SiteID of the image

Range

a list containing range values dor each channel image normalization (see normalize from EBImage)

col.order

the order of colours to be applied when combining channels

channel.choice

channel selection (3 maximum)

disp

'raster' or 'browser'. Where should be the image plotted. See display from EBImage package

TimeCourse

does the image come from timecourse experiment ?

TimePoint

the timepoint of the image. Ignored if TimeCourse=FALSE

returnMat

shall image matrix be returned instead of dispayed ?

CellStep

radius of the circle around from cell center coordinates.

xcoord

x coordinate of cell pixel centroid

ycoord

y coordinate of cell pixel centroid

fullIm

shall full image be returned or cell zoom only?

resize

shall the returned image be resized ?

dim.resize

the size of resized image. Ignored if resize=FALSE

Value

a raster image or Image class element

Author(s)

Allan Sauvat, allan.sauvat@gustaveroussy.fr

Examples

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#Not running
#Bi-parametric plot of cell properties
smoothScatter(log10(GlobalData$Hoechst.Norm),log10(GlobalData$Nuc.Corr),colramp=myRamp,useRaster=T,
nrpoints=0,bandwidth=0.001,nbin=500,ylab='Nuclear Area',xlab='Corrected Hoechst Intensity',main='Debris Segmentation')

#Get coordinates of given point
test = identify(log10(GlobalData$Hoechst.Norm),log10(GlobalData$Nuc.Corr),n=1,plot=F)

#Draw image where cell is found
GetCELL(PlateID = GlobalData$Plate.ID[test],SiteID = GlobalData$Site.ID[test],WellID = GlobalData$Well.ID[test],xcoord = GlobalData$'Pixel Centroid X'[test],ycoord = GlobalData$'Pixel Centroid Y'[test],
           SERVER =SERVER,Range=list(c(0,0.4),c(0,0.1),c(0,0.05)),disp='browser',CellStep = 50, fullIm = T) #Return cell located on plot

Ahlallan/MetaxpR documentation built on March 18, 2020, 6:05 a.m.