cytoskeleton-analyser is a postprocessor for extraction, analysis and human-friendly presentation of the raw binary results generated by Explicit-Microtubules.
Explicit-Microtubules Explicit-Microtubules is a C++ simulator of the whole-cell microtubule system. It reconstructs computationally the microtubule geometry and real-time dynamics in 3d space and time using stochastic algorithms. In the course of the simulation based on a multitude of bioogical information, it outputs detailed histories of microtubule dynamics along with three-dimensional snapshots of microtubules. However, designed to be focuced on versatile generation procedures, Explicit-Microtubules only includes basic data analysis.
Complementing the simulator, cytoskeleton-analyser is designed to extract, analyse and visualize various characteristics of the stochastically reconstructed microtubule system.
Cytoskeleton Analyser requires python 3.9 or later.
When installing by pip, the following dependencies are installed automatically:
Provided that python is present, in the simplest case the Cytoskeleton Analyser may be installed globallly using pip:
pip install cytoskeleton-analyserHowever, the recommended way is installing the package into a python virtual environment, which adds only a few commans:
-
Create a project directory (here named ‘myproject’) and cd to it.
-
Create a python virtual environment (here named ‘venv3.9’).
-
Activate the virtual environment.
-
Install as above.
mkdir myproject && cd myproject
python3 -m venv venv3.9
source venv3.9/bin/activate
pip install cytoskeleton-analyserAlternatively, if you want to install the python package straight from the GitHub repository, replace the last line above with
pip install git+git://github.com/vsukhor/cytoskeleton-analyserA more complete introduction, use examples and API are available in the documentation.`
cytoskeleton-analyser is available under the terms of the BSD 3 Clause license. See LICENSE.txt for more information.