Hi,
I'm new to this mailing list so apologies if this is too basic. I have
confocal images 512x512 from which I have extracted x,y positions of the
coordiates of labelled cells exported from ImageJ as a.csv file. I also
have images that define an underlying pattern in the tissue defined as
areas of different pixel values 0 or 255 (also 512x512) I've exported
these images as .txt files. I'd like to use spatstat to look at how the
individual cells plot onto these patterns.
#I can import my x,y data and do basic stats with spatstat by doing the
following:
library(spatstat)
data01 <- read.csv("250810.csv", skip=1)
x <- data01[[2]]
y <- data01[[3]]
data02 <- ppp(x, y, xrange=c(0,512), yrange=c(0,512))
unitname(data02) <- c("pixel", "pixels")
plot(data02)
#etc etc
#I can also import my text images and convert them to a tessellation
using the following:
a <- read.table("FOLLICLES.txt")
win <- owin(c(0,512), c(0,512))
unitname(win) <- c("pixel", "pixels")
b <- as.matrix(a, xrange=c(0,512), yrange=c(0,512))
unitname(b) <- c("pixel", "pixels")
c <- im(b, xcol=seq(ncol(b)), yrow=seq(nrow(b)), unitname="pixels")
d <- tess(image = c)
plot(d)
#I can then plot my ppp pattern on top of my tessellation using:
plot(d)
plot(data02, add=TRUE)
#So far so good, but when I run for example:
qb <- quadratcount(data02, tess = d)
#I get the following error:
Warning message:
In quadratcount.ppp(data02, tess = d) :
Tessellation does not contain all the points of X
#When I investigate further the following is returned for each object:
> d
Tessellation
Tessellation is determined by a factor-valued image with 2 levels
window: binary image mask
512 x 512 pixel array (ny, nx)
enclosing rectangle: [0.5, 512.5] x [0.5, 512.5] pixels
> data02
planar point pattern: 254 points
window: rectangle = [0, 512] x [0, 512] units
#I don't understand why my tessellation is a different size but even
taking this into account my ppp should plot inside the window and does
when i do plot(data02, add=TRUE). I've spent ages playing around with
redefining the windows but I must be missing something (probably obvious).
Any help would be appreciated, I can provide files.
Kind regards
Richard
