Running the PyFibre GUI

Once installed, enter the PyFibre deployment environment using:

python -m ci shell

and call the executable PyFibre_GUI from the command line to initiate the graphical user interface.

File Viewer

PyFibre is set by default to detect Tagged Image Format (TIF) files. To load in individual files to analyse, use the file window to navigate through your file tree and the ‘Add Files’ button to load in files or folders into the software.

File Management

Once loaded, the files are visible in a scrollable list on the left hand side. They can be removed from here at any time by highlighting and clicking the ‘Delete’ button, or automatically filtered for keywords using the ‘Filter’ entry form.

Running Analysis

Clicking the ‘Run’ button at the bottom will begin a batch analysis of all the files listed within the box at the time of execution. This can be interrupted at any point using the ‘Stop’ button.

Saving Databases

The ‘Save Database’ icon brings up a file window in which to save a collated copy of all loaded image metrics.

Image Viewer

The image display notebook on the right hand side of the GUI is able to show both the original images as well as results of PyFibre’s analysis.

Table 1 Image Viewer

Tab	Description
Loaded Image	Grey-scale multi-channel image
Tensor Image	RGB multi-channel image, using hue, saturation and brightness based on pixel structure tensor
Network	Grey-scale multi-channel image with over-layed FIRE networks
Fibre	Grey-scale multi-channel image with over-layed individual fibres extracted from FIRE networks
Fibre Segment	Grey-scale multi-channel image with over-layed segmented regions base on position of FIRE networks
Cell Segment	Grey-scale multi-channel image with over-layed segmented regions base on position of cellular regions
Metrics	List of measured properties for multi-channel image