README

Table of Contents

1. About The Project
   • Built With
2. Getting Started
   • Prerequisites
   • Installation
3. Usage
4. Contributing
5. Contact

About The Project

The two MATLAB codes are designed to enable user-assisted automated quantification of actin filament properties using single-molecule micrographs.

• The Bundle Analysis program is designed to quantify actin filament crosslinking in a time-lapse movie.
• The Filament Length Quantification program is designed to quantify the lengths of individual actin filaments present in the micrograph.

The work is supported by NIH and by the Genetics and Cell Biology department of University of Minnesota, Twin-cities.

Built With

• MATLAB by Mathworks

Getting Started

To use the codes, the entire repository can be downloaded from the "code" dropdown menu. Please save them in an accessible location in your computer.

Prerequisites

MATLAB by Mathworks needs to be installed and activated.

• Link to download MATLAB - https://www.mathworks.com/downloads/

Installation

MATLAB needs to be configured with several add-on Toolboxes

1. Image Acquisition Toolbox
2. Image Processing Toolbox
3. Signal Processing Toolbox
4. Curve Fitting Toolbox

• To install add-ons, in MATLAB go to the home tab and in the Add-Ons dropdown menu click on "Get Add-Ons". Here you can search for specific toolboxes and install them.

Usage

Use the sample images/movies to trial run the code in your system. To further fine tune the usage of these codes for your need, please go through the User Manual.

For more examples on the application of these programs, you may refer to these publications -

1. Sherer, L. A., & Courtemanche, N. (2022). Cooperative bundling by fascin generates actin structures with architectures that depend on filament length. Frontiers in Cell and Developmental Biology, 10, 974047. https://doi.org/10.3389/fcell.2022.974047
2. Zweifel, M. E., Sherer, L. A., Mahanta, B., & Courtemanche, N. (2021). Nucleation limits the lengths of actin filaments assembled by formin. Biophysical journal, 120(20), 4442-4456. https://doi.org/10.1016/j.bpj.2021.09.003

Contributing

We welcome any contributions you make to the code.

If you have a suggestion that would make this better, please fork the repository and create a pull request.

1. Fork the Project
2. Create your Feature Branch
3. Commit your Changes
4. Push to the Branch
5. Open a Pull Request

Contact

Biswa Mahanta - (www.linkedin.com/in/biswa-mahanta) - [email protected]

Project Link: https://github.com/biswa-mahanta/Actin-Filament-Bundling-Analysis.git

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