Metrics

Metrics are grouped together according to which PyFibre objects they are calculated from (fibre network, fibre segment, cell segment, global image). The 4 database types are:

Fibre Network

Contain metrics calculated from each network of fibres extracted by the FIRE algorithm:

<file-name>_network_metric.h5
<file-name>_network_metric.xls

Table 2 Fibre Network Metrics

Metric	Description	Category
No. Fibres	Number of extracted fibres	Content
Mean Fibre Waviness	Average fibre waviness (length / displacement)	Content
Mean Fibre Length	Average fibre pixel length	Content
Fibre Angle SDI	Angle spectrum SDI (mean / max) of fibre angles	Content
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	Network

Fibre Segment

Contain metrics calculated from each fibre segment identified in the segmentation process:

<file-name>_fibre_metric.h5
<file-name>_fibre_metric.xls

Table 3 Fibre Segment Metrics

Metric	Description	Category
Fibre Segment Area	Area of fibre segment (in pixels)	Shape
Fibre Segment Coverage	Ratio of fibre segment area / bounding box area	Content
Fibre Segment Circularity	Measure of how circular the fibre segment is	Shape
Fibre Segment Eccentricity	Eccentricity shape metric of fibre segment	Shape
Fibre Segment SHG Angle SDI	Angle spectrum SDI (mean / max) for all SHG image pixels in fibre segment	Texture
Fibre Segment SHG Anisotropy	Anisotropy of mean structure tensor of all SHG image pixels in fibre segment	Texture
Fibre Segment SHG Local Anisotropy	Mean anisotropy of structure tensors of all SHG image pixels in fibre segment	Texture
Fibre Segment SHG Mean	Mean intensity of fibre segment pixels in SHG image	Texture
Fibre Segment SHG STD	Standard deviation of fibre segment pixels in SHG image	Texture
Fibre Segment SHG Entropy	Average Shannon entropy of fibre segment pixels in SHG image

Cell Segment

Contain metrics calculated from each cell segment identified in the segmentation process:

<file-name>_cell_metric.h5
<file-name>_cell_metric.xls

Table 4 Cell Segment Metrics

Metric	Description	Category
No. Cells	Number of cell segments	Content
Cell Segment Area	Area of cell segment (in pixels)	Shape
Cell Segment Coverage	Ratio of cell segment area / bounding box area	Content
Cell Segment Circularity	Measure of how circular the cell segment is	Shape
Cell Segment Eccentricity	Eccentricity shape metric of cell segment	Shape
Cell Segment PL Angle SDI	Angle spectrum SDI (mean / max) for all PL image pixels in cell segment	Texture
Cell Segment PL Anisotropy	Anisotropy of mean structure tensor of all PL image pixels in cell segment	Texture
Cell Segment PL Local Anisotropy	Mean anisotropy of structure tensors of all PL image pixels in cell segment	Texture
Cell Segment PL Mean	Mean intensity of cell segment pixels in PL image	Texture
Cell Segment PL STD	Standard deviation of cell segment pixels in PL image	Texture
Cell Segment PL Entropy	Average Shannon entropy of cell segment pixels in PL image

Global Image

Contain metrics calculated from the global image:

<file-name>_global_metric.h5
<file-name>_global_metric.xls

Contains averages of all network and segment metrics that are created during the analysis process

Output Files

PyFibre will create a folder with relevant analysis for each multi image that is loaded into the software. These contain database files containing all metrics for each identified object in the SHG-PL-Trans images in both hdf5 and xls formatting. PNG images displaying the analysis are also created if the --save_figures option is selected:

file-name-shg.tif
file-name-pl.tif
file-name-pyfibre-analysis/
│
├── data
│    │
│    ├── file-name_global_metric.h5
│    ├── file-name_global_metric.xls
│    ├── file-name_cell_metric.h5
│    ├── file-name_cell_metric.xls
│    ├── file-name_fibre_metric.h5
│    ├── file-name_fibre_metric.xls
│    ├── file-name_network_metric.h5
│    ├── file-name_network_metric.xls
│    ├── file-name_network.pkl
│    ├── file-name_fibre_segments.npy
│    └── file-name_cell_segments.npy
│
│
└── fig
     ├── file-name_cell_seg.png
     ├── file-name_fibre_seg.png
     ├── file-name_fibre.png
     ├── file-name_network.png
     ├── file-name_tensor.png
     ├── file-name_PL.png
     ├── file-name_SHG.png
     └── file-name_trans.png

The additional raw data files in the data directory contain serialised copies of the segment and network objects used in the analysis:

file-name_network.pkl

Contains a pickled copy of the NetworkX graph used to represent the fibre networks:

file-name_fibre_segments.npy
file-name_cell_segments.npy

Contain stacks of NumPy arrays representing pixel masks of each fibre and cell segment identified in the segmentation process.

Databases

Databases are also generated from all SHG-PL-Trans images that are loaded into the PyFibre software during a session. The names of these output files can be customised by setting the --database_name flag in the CLI or specifying a name in the “Save Database” GUI tool:

<database_name>_global.h5
<database_name>_global.xls

Contains a set of global metrics for each image:

<database_name>_network.h5
<database_name>_network.xls

Contains metrics for every fibre network in each image:

<database_name>_fibre.h5
<database_name>_fibre.xls

Contains metrics for every fibre segment in each image:

<database_name>_cell.h5
<database_name>_cell.xls

Contains metrics for every cell segment in each image.