2.5D Orientation

Calculate the alignment and intensity of matrix fibers directed toward a cell embedded in a 3D biopolymer, based on 2D images. This measurement serves as an indirect proxy for cell contractility.

Alternatively, the tool can be used to simply quantify the alignment of cells or other structures relative to the x- or y-axis, by ignoring the cell images (set them to None).

• Theory
  • How it works
• Interface
  • Adding Measurements
• Parameters
  • Segmentation
  • Orientation
• API
  • Solver