data(vesicles)
vesicles
is a point pattern
(object of class "ppp"
) representing the location
of the synaptic vesicles. The window of the point pattern
represents the region of presynapse where synaptic vesicles were
observed in this study.
There is a hole in the window, representing the region occupied by
mitochondria, where synaptic vesicles do not occur. The dataset vesicles.extra
is a list with entries
presynapse
outer polygonal boundary of presynapse
mitochondria
polygonal boundary of mitochondria
mask
binary mask representation of vesicles window
activezone
line segment pattern representing
the active zone.
}
vesicles.txt
spatial locations of vesicles
presynapse.txt
vertices of presynapse
mitochondria.txt
vertices of mitochondria
vesiclesimage.tif
greyscale microscope image
vesiclesmask.tif
binary image of mask
activezone.txt
coordinates of activezone
}
The files are in the folder rawdata/vesicles
in the
system.file
, as shown
in the examples.The boundaries for the active zone, mitochondria, pre- and post synaptic terminals, and the centre of the synaptic vesicles were annotated by hand on the image.
plot(vesicles)
with(vesicles.extra,
plot(activezone, add=TRUE, col="red"))
## read coordinates of vesicles from raw data, for training purposes
vf <- system.file("rawdata/vesicles/vesicles.txt", package="spatstat")
vdf <- read.table(vf, header=TRUE)
Run the code above in your browser using DataLab