makeBlock: Model an Embedded Tissue Block With Registration Marks

In TobinH/microTransit: Quantitative Polarized Light Imaging and Analysis Tools

Model an Embedded Tissue Block With Registration Marks

Description

makeBlock creates a "histoBlock" object to register a physical cross-section (typically a histology slide) within a MicroCT volume.

Usage

makeBlock(
  B,
  H,
  L1,
  S1,
  W1,
  Theta1 = 45,
  point1 = TRUE,
  L2,
  S2,
  W2,
  Theta2 = -45,
  point2 = TRUE
)

Arguments

B	Block width on face plane (match to voxel units, usually millimeters).
H	Block height on face plane (match to voxel units, usually millimeters).
L1, L2	Upper and lower longitudinal notch offsets. For each, this is the distance from the nearest lateral face to the far side of the longitudinal notch, as measured on the front or back faces of the block.
S1, S2	Upper and lower oblique notch offsets. Measured from the nearest lateral face to the *near* side of the oblique notch. Lx & Sx should be measured on the same face (front or back).
W1, W2	Upper and lower oblique notch widths, measured orthogonal to oblique notch orientation (essentially the width of the notches as they were machined).
Theta1, Theta2	Angle between longitudinal and oblique notches upper face and lower face. Default is 45 degrees.
point1, point2	Do the upper/lower notches form an arrowhead pointing toward the front face of the block?

Details

This function works together with registerSlide to provide the information necessary to position a section back within the volume of its parent block, e.g. for importing histological images into a microCT volume.

Value

A object of type "histoBlock."

See Also

Other Section Registration Functions: registerSlide()

TobinH/microTransit documentation built on Jan. 19, 2024, 5:21 a.m.