osteo(spatstat)
osteo()所属R语言包：spatstat
Osteocyte Lacunae Data: Replicated Three-Dimensional Point Patterns
骨陷窝数据：复制三维点模式
译者：生物统计家园网 机器人LoveR
描述----------Description----------
These data give the three-dimensional locations of osteocyte lacunae observed in rectangular volumes of solid bone using a confocal microscope.
这些数据给出了矩形固体骨量，使用共聚焦显微镜中观察到的骨陷窝的三维位置。
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.
有4个样品的骨骼，10个区域被映射在每个骨骼，产生40个空间点模式。数据可以被视为重复观测的三维点的过程中，嵌套在骨标本。
用法----------Usage----------
data(osteo)
格式----------Format----------
A hyperframe with the following columns:
Ahyperframe以下几列：
character string identifier of bone sample
字符串标识符的骨骼标本
last numeral in id
最后一个数字id
three dimensional point pattern (class pp3)
三维点模式（类pp3）
Details
详细信息----------Details----------
These data are three-dimensional point patterns representing the positions of osteocyte lacunae, holes in bone which were occupied by osteocytes (bone-building cells) during life.
这些数据是三维的图案，代表骨陷窝的位置，孔骨骨（骨单元）在被占领的生活。
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.
在四个不同的头骨猕猴猴子iusing一个三维显微镜作了观测。从每一个头骨，观察收集了10个独立的采样体积。在所有中，有40个三维点数据集的模式。
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.
数据收集于1984年由A.灸手可热，A. Boyde，CV霍华德与里德（请参阅参考资料），使用串联扫描反射光显微镜（TSRLM）的伦敦大学学院（University College London）。这是一个与第一光学共聚焦显微镜。
Each point pattern dataset gives the (x,y,z) coordinates (in microns) of all points visible in a three-dimensional rectangular box (“brick”) of dimensions 81 * 100 * d microns, where d varies. The z coordinate is depth into the bone (depth of the focal plane of the confocal microscope); the (x,y) plane is parallel to the exterior surface of the bone; the relative orientation of the x and y axes is not important.
每个点图案数据集给出(x,y,z)坐标（以微米为单位）可见的所有点在一个三维的矩形框（“砖”）的尺寸81 * 100 * d微米，其中d变化。坐标是z深度到骨（深度的共聚焦显微镜的焦平面）;(x,y)平面是平行于骨的外表面的相对取向x 和y轴并不重要。
The bone samples were three intact skulls and one skull cap, all originally identified as belonging to the macaque monkey 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.
骨标本3个完整的头骨和一个头盖骨，原本被认定为属于猕猴食蟹猴，从收集，伦敦大学人体解剖学教研室。后来分析（巴德利等，1993），这里给出的第一个动物的头盖骨，是一个不同的亚种，解剖检验证实了这一点。
取样程序----------Sampling Procedure----------
The following extract from Baddeley et al (1987) describes the sampling procedure.
以下提取从巴德利等人（1987）描述的采样过程。
The parietal bones of three fully articulated adult Macaque monkey (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 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.
充分阐述三个成年猕猴（食蟹猴）从伦敦大学学院（University College London）的收集头骨的顶骨。右顶骨进行了检查，在每一种情况下，约1厘米的矢状缝和冠状缝后方2厘米外侧。被安装在橡皮泥上放置一个移动舞台下的TSRLM的头骨。浸油和X 60，NA 1.0油浸物镜（LOMO），主要集中在10微米以下的颅骨表面。电视图像是由一台松下WB 1850 / B相机在索尼PVM 90CE电视监视器。
A graduated rectangular counting frame 90 * 110 mm (representing 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.
一个毕业的矩形计数帧90 * 110毫米（代表82 * 100微米的实际单位）被标记上的有机玻璃覆盖，并固定在屏幕上。组织定义了一个子场的帧内看到的面积：10毫米宽的时间是一个保护区上显示的帧的所有侧面。十个子场进行了检查，约在矩形网格图案排列，与每个字段对分离的至少一个字段的宽度。通过应用一个随机生成的坐标转移到移动阶段，初始场的位置是随机决定的。后续字段均达到使用的粗控制的显微镜载物台上，在按照与矩形栅格图案。
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 d was recorded. The 3-dimensional sampling volume was therefore a rectangular box of dimensions 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 x and 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.
对于每个子场，焦平面横移，从它的初始的10微米的深度，直到所有可见骨陷窝已审查。这个深度d被记录下来。 3维采样体积为一个矩形框的尺寸82 * 100 * d微米，因此被称为“砖”。对于每一个可见的空白，精细调焦传动控制，调整，直到达到最大亮度。焦平面的深度，然后记录为$ Z坐标的“中心点”的空白。在不移动焦点平面的情况下，x和y腔隙性图像的中心坐标读出刻度计数帧。这需要一个主观判断的2维图像的中心的位置。剖面近似椭圆形，中心被认为是良好定义的。由独立的重复（由同一操作和由不同的运营商）的记录程序的精度进行了测试，并发现是加或减2毫米在屏幕上重现。
A lacuna was counted only if its (x, y) coordinates lay inside the 90 * 110 mm counting frame.
一个陷窝计数，只有当它的(x, y)90 * 110mm计数框架内坐标奠定。
源----------Source----------
Adrian Baddeley.
阿德里安·巴德利。
参考文献----------References----------
Three dimensional analysis of the spatial distribution of particles using the tandem-scanning reflected light microscope. Acta Stereologica 6 (supplement II) 87–100.
Analysis of a three-dimensional point pattern with replication. Applied Statistics 42 (1993) 641–668.
Unbiased estimation of particle density in the tandem-scanning reflected light microscope. Journal of Microscopy 138 203–212.
实例----------Examples----------
data(osteo)
osteo
## Not run: [＃不运行：]
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)))
## End(Not run)[＃（不执行）]
转载请注明:出自 生物统计家园网(http://www.biostatistic.net)。
注：
注1：为了方便大家学习，本文档为生物统计家园网机器人LoveR翻译而成，仅供个人R语言学习参考使用，生物统计家园保留版权。
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发表于 2012-9-30 13:51:49
