Stereology Analysis

Usage

stereology(
  data,
  intersections,
  totalPoints,
  boundaryIntersections = NULL,
  objectCount = NULL,
  referenceArea,
  sectionThickness = 5,
  gridSpacing,
  tissueType = "vessels",
  groupVar = NULL,
  calculateAa = TRUE,
  calculateVv = TRUE,
  calculateBa = FALSE,
  calculateNa = FALSE,
  calculateSv = FALSE,
  showConfidenceIntervals = TRUE,
  bootstrapIterations = 1000,
  showGroupComparison = FALSE,
  showDescriptives = TRUE,
  showPlot = TRUE,
  plotType = "bars",
  showMethodology = TRUE,
  showReferences = FALSE
)

Arguments

data: .
intersections: Number of grid intersections (hits) with the structure of interest (e.g., vessels, nuclei, fibrosis areas).
totalPoints: Total number of grid points or test lines used in the measurement.
boundaryIntersections: Number of grid line intersections with object boundaries (for boundary density calculation).
objectCount: Number of discrete objects counted (for numerical density calculation).
referenceArea: Total reference area examined (in square micrometers). Typically calculated as: image width × height.
sectionThickness: Histological section thickness in micrometers. Required for volume density calculations. Default: 5 μm.
gridSpacing: Distance between grid lines in micrometers. Used for length calculations in boundary/surface density.
tissueType: Type of tissue structure being quantified. This helps provide context-specific interpretation.
groupVar: Optional grouping variable to compare stereology parameters across groups (e.g., diagnosis, treatment, grade).
calculateAa: Area density: proportion of reference area occupied by structure. Formula: Aa = intersection count / total points.
calculateVv: Volume density: proportion of reference volume occupied by structure. In isotropic sections, Vv = Aa.
calculateBa: Boundary density: boundary length per unit area. Requires boundary intersection data.
calculateNa: Numerical density: number of objects per unit area. Requires object count data.
calculateSv: Surface density: surface area per unit volume. Formula: Sv = 2 × Ba (for isotropic sections).
showConfidenceIntervals: Calculate and display 95\ intervals for stereological estimates using bootstrap methods.
bootstrapIterations: Number of bootstrap iterations for confidence interval estimation.
showGroupComparison: Compare stereological parameters across groups (requires grouping variable).
showDescriptives: .
showPlot: Display bar chart of stereological parameters with confidence intervals.
plotType: .
showMethodology: Display detailed explanation of stereological methods, formulas, and interpretation guidelines.
showReferences: Display literature references for stereological methods.

Value

A results object containing:

`results$descriptives`					a table
`results$stereologyTable`					a table
`results$groupComparison`					a table
`results$groupTests`					a table
`results$plot`					an image
`results$methodology`					a html
`results$references`					a html

Tables can be converted to data frames with asDF or as.data.frame. For example:

results$descriptives$asDF

as.data.frame(results$descriptives)