segmentXman is called by the function segmentAllSpots
to segment the single image of one spot.
Usage
segmentXman(x, uname, p, access, spot = NULL)
Arguments
x
A imageHTS object.
uname
A character vector, containing the well names to segment. See
getUnames for details.
p
List of parameters which are read from the file specified in
segmentationPar of the segmentWells function.
access
A character string indicating how to access the data. Valid
values are 'local', 'server' and 'cache', the default.
See fileHTS for details.
spot
An single integer, indicating the spot number to segment. If it
is specified, the default 1 will automatically be used.
Value
Returns a list with the following items
cal: calibrated RGB image of the different channels
nseg: nuclear segmentation mask
cseg: cell segmentation mask
## see also section 2.1 "Image processing on cluster"
localPath <- tempdir()
serverURL <- system.file("extdata", package = "PGPC")
x <- parseImageConf(file.path("conf", "imageconf.txt"),
localPath=localPath,
serverURL=serverURL)
well <- "045-01-C23"
## get segmentation parameter
p <- readHTS(x, type = "file",
filename = file.path("conf", "segmentationpar.txt"),
format = "dcf")
segmentation <- segmentXman(x, well, p, access="cache", spot=1)
Results
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> library(PGPC)
Loading required package: EBImage
Loading required package: imageHTS
Loading required package: cellHTS2
Loading required package: RColorBrewer
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
rbind, rownames, sapply, setdiff, sort, table, tapply, union,
unique, unsplit
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Attaching package: 'Biobase'
The following object is masked from 'package:EBImage':
channel
Loading required package: genefilter
Loading required package: splots
Loading required package: vsn
Loading required package: hwriter
Loading required package: locfit
locfit 1.5-9.1 2013-03-22
Loading required package: grid
Loading required package: SearchTrees
Loading required package: limma
Attaching package: 'limma'
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plotMA
Loading required package: gplots
Attaching package: 'gplots'
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lowess
Loading required package: ggplot2
Attaching package: 'ggplot2'
The following object is masked from 'package:cellHTS2':
annotate
Loading required package: geneplotter
Loading required package: lattice
Loading required package: annotate
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: IRanges
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:gplots':
space
The following objects are masked from 'package:base':
colMeans, colSums, expand.grid, rowMeans, rowSums
Attaching package: 'IRanges'
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resize, tile
Loading required package: XML
Loading required package: ChemmineR
Attaching package: 'ChemmineR'
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fold
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makeUnique
Loading required package: reshape2
Loading required package: plyr
Attaching package: 'plyr'
The following object is masked from 'package:IRanges':
desc
The following object is masked from 'package:S4Vectors':
rename
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/PGPC/segmentXman.Rd_%03d_medium.png", width=480, height=480)
> ### Name: segmentXman
> ### Title: Function used to segment a single image
> ### Aliases: segmentXman
>
> ### ** Examples
>
> ## see also section 2.1 "Image processing on cluster"
> localPath <- tempdir()
> serverURL <- system.file("extdata", package = "PGPC")
>
> x <- parseImageConf(file.path("conf", "imageconf.txt"),
+ localPath=localPath,
+ serverURL=serverURL)
File "conf/imageconf.txt" read.
Number of plates= 48
Number of replicates= 2
Number of wells= 384
Number of channels= 2
Number of spots= 4
>
> well <- "045-01-C23"
>
> ## get segmentation parameter
> p <- readHTS(x, type = "file",
+ filename = file.path("conf", "segmentationpar.txt"),
+ format = "dcf")
>
> segmentation <- segmentXman(x, well, p, access="cache", spot=1)
segmentAllSpots 48 24 0.0007 0.00025 0.0001 0.005 100 3000 15000 150 724 1324 724 1324 400 TRUE TRUE TRUE TRUE
read images
smooth image
computing nseg
segmenting cells using Voronoi tesselation
segmentation OK
Warning messages:
1: In readTIFF(x, all = all, ...) :
TIFFReadDirectory: Unknown field with tag 65400 (0xff78) encountered
2: In readTIFF(x, all = all, ...) :
TIFFReadDirectory: Unknown field with tag 65400 (0xff78) encountered
>
>
>
>
>
> dev.off()
null device
1
>