Metrics

PyFibre calculates properties for the global images and each segmented region. The resultant databases for each section are then labelled:

``{directory}/data/{prefix}_global.h5`` = global image output (also in .xls format)
``{directory}/data/{prefix}_fibre.h5`` = fibre segmented image output (also in .xls format)
``{directory}/data/{prefix}_network.h5`` = fibre networks output (also in .xls format)
``{directory}/data/{prefix}_cell.h5`` = cell segmented image output (also in .xls format)

The database metrics have the following columns:

Table 2 SHG-PL-Trans Image Metrics

Metric	Description	Category
No. Fibres	Number of extracted fibres	Content
Fibre Waviness	Average fibre waviness (length / displacement)	Content
Fibre Lengths	Average fibre pixel length	Content
Fibre Angles	Average fibre angle	Content
Fibre Segment Coverage	Ratio of image containing fibres	Content
Fibre Segment Area	Area of image (in pixels) containing fibres	Shape
Fibre Segment Linearity	Average ratio of diameter to perimeter for fibre segments	Shape
Fibre Segment Eccentricity	Average eccentricity metric of fibre segments	Shape
Fibre Segment SHG Angle SDI	Angle spectrum SDI (mean / max) for all SHG image pixels in fibre regions	Texture
Fibre Segment SHG Anisotropy	Anisotropy of structure tensor for all SHG image pixels in fibre regions	Texture
Fibre Segment SHG Pixel Anisotropy	Mean anisotropy of structure tensor for all SHG image pixels in fibre regions	Texture
Fibre Segment SHG Mean	Mean pixel intensity of SHG image in fibre segment	Texture
Fibre Segment SHG STD	Standard deviation of pixel intensity of SHG image in fibre segment	Texture
Fibre Segment SHG Entropy	Average Shannon entropy of pixel intensities of SHG image in fibre segment	Texture
Fibre Network Degree	Average fibre network number of edges per node	Network
Fibre Network Eigenvalue	Max eigenvalue of network adjacency matrix	Network
Fibre Network Connectivity	Average fibre network connectivity	Network
Fibre Network Cross-Link Density	Average cross-links per fibre	Content
No. Cells	Number of cell segments	Content
Cell Segment Coverage	Ratio of image containing fibres/cells	Content
Cell Segment Area	Area of image (in pixels) containing cells	Shape
Cell Segment Linearity	Average ratio of diameter to perimeter for cell segments	Shape
Cell Segment Eccentricity	Average eccentricity metric of cell segments	Shape
Cell Segment PL Angle SDI	Angle spectrum SDI (mean / max) for all PL image pixels in cell regions	Texture
Cell Segment PL Anisotropy	Anisotropy of structure tensor for all PL image pixels in cell regions	Texture
Cell Segment PL Pixel Anisotropy	Mean anisotropy of structure tensor for all PL image pixels in cell regions	Texture
Cell Segment PL Intensity Mean	Mean pixel intensity of PL image in cell segment	Texture
Cell Segment PL Intensity STD	Standard deviation of pixel intensity of PL image in cell segment	Texture
Cell Segment PL Intensity Entropy	Average Shannon entropy of pixel intensities of PL image in cell segment	Texture