https://github.com/cran/spatstat
Revision 4fe059206e698a4b7135d792f3d533b173ecfe77 authored by Adrian Baddeley on 16 May 2012, 12:44:15 UTC, committed by cran-robot on 16 May 2012, 12:44:15 UTC
1 parent df59a11
Tip revision: 4fe059206e698a4b7135d792f3d533b173ecfe77 authored by Adrian Baddeley on 16 May 2012, 12:44:15 UTC
version 1.27-0
version 1.27-0
Tip revision: 4fe0592
osteo.Rd
\name{osteo}
\alias{osteo}
\docType{data}
\title{
Osteocyte Lacunae Data: Replicated Three-Dimensional Point Patterns
}
\description{
These data give the three-dimensional locations of
osteocyte lacunae observed in rectangular volumes of
solid bone using a confocal microscope.
There were four samples of bone, and ten regions were mapped
in each bone, yielding 40 spatial point patterns.
The data can be regarded as replicated observations of a
three-dimensional point process, nested within bone samples.
}
\usage{data(osteo)}
\format{
A \code{\link{hyperframe}} with the following columns:
\tabular{ll}{
\code{id} \tab character string identifier of bone sample \cr
\code{shortid} \tab last numeral in \code{id} \cr
\code{brick} \tab serial number (1 to 10) of sampling volume within
this bone sample \cr
\code{pts} \tab three dimensional point pattern (class \code{pp3}) \cr
\code{depth} \tab the depth of the brick in microns
}
}
\details{
These data are three-dimensional point patterns
representing the positions of \emph{osteocyte lacunae}, holes
in bone which were occupied by osteocytes (bone-building cells) during life.
Observations were made on four different skulls of Macaque monkeys
iusing a three-dimensional microscope.
From each skull, observations were collected in 10 separate sampling volumes.
In all, there are 40 three-dimensional point patterns in the dataset.
The data were collected in 1984
by A. Baddeley, A. Boyde, C.V. Howard and S. Reid
(see references) using the tandem-scanning reflected light microscope
(TSRLM) at University College London. This was one of the first
optical confocal microscopes available.
Each point pattern dataset gives the \eqn{(x,y,z)} coordinates
(in microns) of all points visible in a
three-dimensional rectangular box (``brick'') of dimensions
\eqn{81 \times 100 \times d}{81 * 100 * d} microns,
where \eqn{d} varies.
The \eqn{z} coordinate is depth into the bone
(depth of the focal plane of the confocal microscope); the \eqn{(x,y)}
plane is parallel to the exterior surface of the bone;
the relative orientation of the \eqn{x} and \eqn{y} axes is not important.
The bone samples were three intact skulls and one skull
cap, all originally identified as belonging to the macaque monkey
\emph{Macaca fascicularis}, from the collection of the
Department of Anatomy, University of London. Later analysis
(Baddeley et al, 1993) suggested that the skull cap, given here as
the first animal, was a different subspecies, and this was confirmed by
anatomical inspection.
}
\section{Sampling Procedure}{
The following extract from Baddeley et al (1987)
describes the sampling procedure.
The parietal bones of three fully articulated adult Macaque monkey
\emph{(Macaca fascicularis)} skulls from the collection of
University College London were used. The right parietal bone was
examined, in each case, approximately 1 cm lateral to the sagittal
suture and 2 cm posterior to the coronal suture. The skulls were
mounted on plasticine on a moving stage placed beneath the TSRLM.
Immersion oil was applied and a \eqn{\times 60}{X 60}, NA 1.0 oil immersion
objective lens (Lomo) was focussed at 10 microns below the cranial
surface. The TV image was produced by a Panasonic WB 1850/B camera
on a Sony PVM 90CE TV monitor.
A graduated rectangular counting frame
\eqn{90 \times 110}{90 * 110} mm (representing
\eqn{82 \times 100}{82 * 100} microns in real units)
was marked on a Perspex overlay
and fixed to the screen. The area of tissue seen within the frame defined
a subfield: a guard area of 10 mm width was visible on all sides of the
frame. Ten subfields were examined, arranged approximately in
a rectangular grid pattern, with at least one field width separating
each pair of fields. The initial field position was determined randomly
by applying a randomly-generated coordinate shift to the moving stage.
Subsequent fields were attained
using the coarse controls of the microscope stage, in accordance with
the rectangular grid pattern.
For each subfield, the focal plane was racked down from its initial
10 micron depth until all visible osteocyte lacunae had been examined.
This depth \eqn{d} was recorded. The 3-dimensional sampling volume was
therefore a rectangular box of dimensions
\eqn{82 \times 100 \times d}{82 * 100 * d} microns,
called a ``brick''.
For each visible lacuna, the fine focus racking control was adjusted until
maximum brightness was obtained. The depth of the focal plane was then
recorded as the $z$ coordinate of the ``centre point'' of the
lacuna. Without moving the focal plane, the \eqn{x} and \eqn{y}
coordinates of
the centre of the lacunar image were read off the graduated counting frame.
This required a subjective judgement of the position of the centre of the
2-dimensional image. Profiles were approximately elliptical and the centre
was considered to be well-defined. Accuracy of
the recording procedure was tested by independent repetition (by the
same operator and by different operators) and found to be reproducible
to plus or minus 2 mm on the screen.
A lacuna was counted only if its \eqn{(x, y)} coordinates lay inside
the \eqn{90 \times 110}{90 * 110} mm counting frame.
}
\source{
Adrian Baddeley.
}
\references{
Baddeley, A.J., Howard, C.V, Boyde, A. and Reid, S.A. (1987)
Three dimensional analysis of the spatial distribution of
particles using the tandem-scanning reflected light microscope.
\emph{Acta Stereologica} \bold{6} (supplement II) 87--100.
Baddeley, A.J., Moyeed, R.A., Howard, C.V. and Boyde, A. (1993)
Analysis of a three-dimensional point pattern
with replication.
\emph{Applied Statistics} \bold{42} (1993) 641--668.
Howard, C.V. and Reid, S. and Baddeley, A.J. and Boyde, A. (1985)
Unbiased estimation of particle density
in the tandem-scanning reflected light microscope.
\emph{Journal of Microscopy} \bold{138} 203--212.
}
\examples{
data(osteo)
osteo
\dontrun{
plot(osteo$pts[[1]], main="animal 1, brick 1")
ape1 <- osteo[osteo$shortid==4, ]
plot(ape1, tick.marks=FALSE)
with(osteo, summary(pts)$intensity)
plot(with(ape1, K3est(pts)))
}
}
\keyword{datasets}
Computing file changes ...