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.
}
All coordinates are in nanometres (nm).
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)
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