This package contains a tool automembrane which employs automatic differentiation to compute the energy and forces of the membrane given a 2D discrete shape profile.
We apply the tool to a dataset where ActuAtor is used to deform the nuclear membrane.
A preprint of this work is available on the bioRxiv.
ActuAtorForceEstimation
├── actuator_example -> Code for application to ActuAtor
│ ├── coordinates -> Initial segmentations
│ ├── crop_images -> Cropped images
│ └── raw_images -> Raw EM images
├── automembrane -> Source for automembrane tool
│ └── tests
├── devtools
│ └── conda-envs
└── examplesAfter cloning this repository, automembrane can be installed by running pip install . from the root folder.
Examples can be found in the actuator_example folder.
The raw/cropped EM images and segmentations are in the corresponding subfolders.
There are several python files which perform the analysis and work.
actuator_constants.py -> Contains mappings for file locations and EM image metadata
make_movie.py -> Helper for making movies
main_sweep.py -> Main driver function which runs relaxation, parameter variation and plotting
The following should be run in order:
variation_relax.py -> Code for relaxation of initial segmentented geometries
variation_run.py -> Runs parameter variation on the relaxed geometries
variation_view.py -> Generated plots and moviesIf you are short on time, you can simply run main_sweep.py which will perform geometric relaxation, parameter variation, and plotting for you automatically.
It calls functions from the three variations_*.py files which do the actual work.
For a guided approach, there are also two jupyter notebooks which discuss the theory behind the work. You can also execute these to get a feel for what is happening in the automatic scripts.
Copyright (c) 2022-2023, Eleanor Jung, Cuncheng Zhu, Christopher T. Lee, and Padmini Rangamani
Project based on the Computational Molecular Science Python Cookiecutter version 1.6.