4D Cell Membrane Visualization and Quantification

Visualization and quantification of spatiotemporal membrane signaling

This MATLAB package is used to extract, visualize, and quantify spatiotemporal membrane signaling of time resolved 3D confocal microscopy observed single cells. It provides

- basic cell parameter, such as cell volume and membrane area

- 3D animation of extracted membrane signaling

- Mollweide projected 2D animation of extracted membrane signaling

- detrended fluctuation analysis (DFA) for each membrane site, quantification and 2D Mollweide projected map of DFA parameter

- preparation for WAVOS (Morlet Wavelet) analysis

- an example dataset of a Dictyostelium cell

CITING: Please cite the following papers when using this code:

1) Hörning, M. and Shibata, T. (2019). Three-Dimensional Cell Geometry Controls Excitable Membrane Signaling in Dictyostelium Cells. Biophysical Journal 116, 372–382. https://doi.org/10.1016/j.bpj.2018.12.012

2) Hörning, M., Bullmann, T. and Shibata, T. (2021). Local membrane curvature pins and guides excitable membrane waves in chemotactic and macropinocytic cells - biomedical insights from an innovative simple model. Frontiers in Cell and Developmental Biology, 9, 2467. https://doi.org/10.3389/fcell.2021.670943

The following open sources have been used:

Mesh Generator:

Persson, P.-o. and Strang, G. (2004). A Simple Mesh Generator in MATLAB. SIAM Review 46, 2004

Download: http://persson.berkeley.edu/distmesh/

Detrended Fluctuation Analysis:

Abrar Habib (2017). r-DFA : Robust Detrended Fluctuation Analysis

https://www.mathworks.com/matlabcentral/fileexchange/60026-r-dfa-robust-detrended-fluctuation-analysis, MATLAB Central File Exchange