example3_history.rst

Example 3: Examination of microtubule dynamic instability

The code snippet below shows a scenario for analysis of the microtubule dynamics where only duration, spatial_maps and event_collections features are selected.

from cytoskeleton_analyser.inout import Paths      # simulation-specific paths
from cytoskeleton_analyser.history.drivers import process  # driver fuction
from sim_specs import cell, data_in, data_out, rinds

params = {
   'edge_len': 0.008,     # (μm) length of filament edge.
   'cell': cell,          # cell object
}

# Specify features to process. If this is None,
# all features are included.
features = [
   'duration',
   'spatial_maps',
   'event_collections',
]

if __name__ == '__main__':

   for ci in rinds:
      paths = Paths(data_in, data_out, params['cell'], ci)
      process(paths, ci, 1, params, True, features)