Orientation

sigma_tensor

Windowsize, in which individual structure elements are calculated. Should be in the range of the underlying structure and can be optimised per setup by performing a test-series.

edge

Pixel width of the edges left blank because alignment cannot be calculated there. Default is 20 px.

max_dist

(Optional) Specify a maximum distance around the cell center for analysis (in px). Default is None.

ignore_cell_outline

By default, the cell-occupied area is excluded, and matrix alignment is calculated only in the remaining area. To analyze alignment across the entire field of view (e.g., relative to the x- or y-axis), set this parameter to True. Default is False.

sigma_first_blur

Initial slight Gaussian blur applied to the fiber image before structure analysis. Default is 0.5.

angle_sections

Angle sections around the cell in degrees, used for polarity analysis of matrix fiber orientation. Default is 5°.

shell_width

Distance shells around the cell for analyzing intensity and orientation propagation over distance. Default is 5 µm.