MyoBand

Simulation and analysis of A bands in myofibril imaging written in Python.

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MyoBand in the Python repository

Simulation

Run python3 simulation.py to simulate A bands.

Analysis

Get the skeletons of the A bands by running python3 get_skeletons.py -d DATA_LOCATION

Installation

• Install with pip install myoband
• Clone this repo in order to use examples

Details

• For A band creation see A_band.py in tests folder.
• An A band is created by adding thickness to a polynomial. The polynomial is created using a random walk (see randomwalk.py).
• A Slide is a 2D array of zeros. A_Bands are then added, forming a mask array. The slide can be viewed using myoband.plotting.imshow(example_slide).
• Gaussian noise can be added and removed (see skeleton_example.py, in which the robustness of the programme is benchmarked).

• Contours of the A bands can be extracted. This feature is used to extract the separate A bands from the image slide.

• Run get_skeletons.py to extract (a) a mask representation of the skeletons and (b) a list of points of the skeletons.

Copyright, 23 March 2023, Henry Joseph Sheehy. All rights reserved.