axonemalyze

Calculate the circularity of axoneme picks from cryo-ET images.

Installation

You can install the axonemalyze by performing the following command:

pip install axonemalyze

Functions

The code is split into two command-line functions:

• segment_axonemes
• estimate_circularity

Installing the package gives access to these functions. The command-line functions are to be run in that order.

For more help with these functions, use the -h flag.

segment_axonemes

The function takes a directory as input. This directory should contain all files in the .coords format with the xyz coordinates of the picks.

Here is an example of how to run this function:

segment_axonemes test_data/

This function outputs a directory (default segmented/) in the input directory with a single .csv file per axoneme.

estimate_circularity

This function takes a directory as input. This directory should contain all files in the .csv format as outputted by segment_axonemes.py.

Here is an example of how to run this function:

estimate_circularity test_data/segmented/

This function prints an average circularity for each axoneme that contains at least five doublets to the standard output.