This is a tutorial on how to locate clumps of pixels by joining adjacent pixels
The images are assumed to be loaded already.
library(RCon3D)
path <- "/Data"
imgs <- findIMG(path)
Set kern.smooth
to smooth the images prior to finding aggregates (Recommended).
agg <- clumps(imgs, channels = "xan", kern.smooth = c(3,3,3), zstep = 0.25, pwidth = 0.75)
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Giving the function zstep
and pwidth
in microns draws the plot to scale.
Here we set a threshold of 100 cubic microns. Clumps smaller than this are not plotted. If thresh.m = FALSE
it would set the threshold to 100 pixels instead.
By default the clumps are coloured by their clump ID. Colours are recycled.
Note that the plot is an interactive 3D plot, and is therefore not visible in this tutorial.
clumps_plot(agg, zstep = 0.25, pwidth = 0.75, thresh = 100, thresh.m = TRUE)
agg[[1]]
contains a data.frame with information on each aggregate/clump
mydf <- agg[[1]]
hist(log10(mydf$Size))
Because we gave the zstep
and pwidth
to the clumps
function we also get the size in cubic microns:
hist(log10(mydf$Size.micron))