Software

Image Processing Tools

TipTracker Code.

Enables sub-pixel (nanometer-scale) dynamic tracking of fluorescently-labeled dynamic polymers with simultaneous end-structure measurement for multi-filament polymers, such as microtubules.
Demonstrated ~36nm measurement accuracy in vivo using LLCPK1 epithelial cells expressing GFP-tubulin (Demchouk et al., 2011) and ~15nm accuracy for in vitro purified tubulin (Gardner et al., 2011).
A subsequent modification enables the code to obtain similar measurements from cells expressing fluorescently-labeped end-binding (EB) proteins (Seetapun et al., 2012).
Supported version contains modifications to accommodate a variety of experimental conditions, and is provided as two Matlab files (function and call script) and support manual (.pdf), and is compatible with multiple data types using the Bio-Formats reader and Tiffread function.

Current supported version

Prahl L.S., Castle B.T., Gardner M.K., Odde D.J. "Quantitative analysis of microtubule self-assembly kinetics and tip structure," Methods in Enzymology, 2014, 540:35-52.

TipTracker_v3

Original publication

Demchouk A., Gardner M.K., and Odde D.J. “Microtubule tip tracking and tip structures at the nanometer scale using digital fluorescence microscopy,” Cellular and Molecular Bioengineering, 2011, 4:192-204.

Tip tracker1_2 Tiffread

FlowTrack Code

BeadTrack Code

Model Convolution Plugin

This plugin is designed to facilitate comparisons between stochastic simulations of cellular processes and digital fluorescence images obtained in cells by applying estimated imaging system blur and noise to simulated data.
Model convolution is similar process to image deconvolution, which can fail to accurately measure the underlying fluorophore distribution under certain circumstances (Gardner et al., 2010).
This technique is designed to provide a direct "apples to apples" statistical comparison of theory and experiment, such as done previously in studies of chromosome congression in mitotic budding yeast (Gardner et al., 2008).
Downloadable plugin is supported by ImageJ.

Reference publication

Gardner M.K., and Odde D.J. “Stochastic simulation and graphic visualization of mitotic processes,” Methods, 2010, 51:251-256.

Model Convolution Plugin

Stochastic Simulations of Cellular Processes

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Cell Migration Simulator, version 1.0 (CMSv1.0)

The cell migration simulator is based on the motor-clutch model for stiffness sensitive cell traction force generation.
CMSv1.0 extends this model to incorporate actin-based protrusion dynamics, cytoskeletal compliance, mass conservation, and force balances to reproduce cell polarization and random motility in a 2D compliant microenvironment.
CMSv1.0 has been featured in recent publications where it replicates cell migration behaviors in microenvironments of varying stiffness (Bangasser et al., Nat. Comm., 2017) and adhesiveness (Klank et al,. Cell Rep., 2017).
The simulation code contains four Matlab files: the base code as a function (cms2Dv1_0.m), shell scripts for standard and paralell computing (cms2D_shell.m and cms2D_par_shell.m), and an analysis code (analyzeCMSoutputv1_0.m). A readme file is also included in the download folder.

Reference publications

Bangasser B.L., Shamsan G.A., Chan C.E., Opoku K.N., Tüzel E., Schlichtmann B.W., Kasim J.A., Fuller B.J., McCullough B.R., Rosenfeld S.S, andOdde D.J. "Shifting the optimal stiffness for cell migration." Nature Communications, 2017, 8: 15313.

Cms v1.0

Kolade Adebowale, Ze Gong, Jay C. Hou, Katrina M. Wisdom, Damien Garbett, Hong-pyo Lee, Sungmin Nam, Tobias Meyer, David J. Odde, Vivek B. Shenoy, Ovijit Chaudhuri, "Enhanced substrate stress relaxation promotes filopodia-mediated cell migration," Nature Materials, 2021.

Cell2D (C++)

Sung Hoon Lee, Jay Hou, Archer Hamidzadeh, Sulaiman M. Yousafzai, Visar Ajeti, Hao Chang, Michael Murrell, David Odde, Andre Levchenko. "A molecular clock controls periodically driven cell migration in confined spaces." Cell Systems (2022)

Confined_migration_code

Motor-Clutch Model for Cell Traction

Stochastic simulator for traction force generation based on the motor-clutch hypothesis, where actomyosin-based traction forces are transmitted to a compliant substrate through dynamic clutch bonds (Chan & Odde, 2008).
Simulated cells are described by eight adjustable parameters — three for motors, five for clutches — plus a substrate of variable stiffness.
The model captures a range of cellular mechanosensing behaviors by changing the operating parameters of motors and clutches (Bangasser et al., 2013).
Simulation is provided as two separate Matlab codes. Running the simulation at a single stiffness (motorclutch1_1.m) enables analysis of cell traction dynamics by visualizing individual "load and fail" events (Chan & Odde, 2008).
A second code (motorclutch2_3.m) outputs traction force and retrograde flow values over a range of substrate stiffness.
A more recent version of the motor clutch model (Mekhdjian et al., 2017) is also available.

Reference publications

Bangasser B.L., Rosenfeld S.S., and Odde, D.J. "Determinants of maximal force transmission in a motor-clutch model of cell traction in a compliant microenvironment," Biophysical Journal, 2013, 105:581-592.

motorclutch1_1 motorclutch2_3

Mekhdjian, A. H.; Kai, F. B.; Rubashkin, M. G.; Prahl, L. S.; Przybyla, L. M.; McGregor, A. L.; Bell, E. S.; Matthew Barnes, J.; DuFort, C. C.; Ou, G.; et al. "Integrin-Mediated Traction Force Enhances Paxillin Molecular Associations and Adhesion Dynamics That Increase the Invasiveness of Tumor Cells into a Three-Dimensional Extracellular Matrix". Molecular Biology of the Cell, 2017, 28(11):1467-1488.

1D_motorclutch_model

S.J. Tan, A.C. Chang, C.M. Miller, S.M. Anderson, L.S. Prahl, D.J. Odde, A.R. Dunn, Regulation and dynamics of force transmission at individual cell-matrix adhesion bonds, Science Advances, 2020.

Cyclic6

Motor Clutch Model — Kelvin-Voigt substrate

MC1D_maxwellsub

xsub_kv_ode_noloop

Mechanochemical Microtubule Assembly Model

Monte Carlo simulator of microtubule assembly dynamics that can be used to predict microtubule (or other multi-filament) polymer assembly behaviors at the level of individual subunit addition and loss events (VanBuren et al., 2002).
Adjustable parameters represent kinetic rates of tubulin dimer association and GTP hydrolysis, free energy values of lateral and longitudinal bonds between tubulin dimers, and concentration of soluble tubulin, and may be individually manipulated to tune simulated dynamic instability behaviors.
Distributed code includes association rate penalties based on local tip structure (Castle & Odde, 2013) and 'pseudo-mechano-chemical' rules to simulate mechanical strain on bonds within the lattice (VanBuren et al., 2002; 2005).
Model code is provided as two Matlab files - an initiation script and the simulator written as a function - plus associated documentation.

Reference publication

VanBuren V., Odde D.J., and Cassimeris L.U. "Estimates of lateral and longitudinal energies within the microtubule lattice," Proceedings of the National Academy of Sciences USA, 2002, 99:6035-6040. Correction in 2004, 101:14989.

Image Processing Tools

TipTracker Code.

TipTracker Code.

FlowTrack Code

FlowTrack Code

BeadTrack Code

BeadTrack Code

Model Convolution Plugin

Model Convolution Plugin

Stochastic Simulations of Cellular Processes

Cell Migration Simulator, version 1.0 (CMSv1.0)

Cell Migration Simulator, version 1.0 (CMSv1.0)

Reference publications

Motor-Clutch Model for Cell Traction

Motor-Clutch Model for Cell Traction

Mechanochemical Microtubule Assembly Model

Mechanochemical Microtubule Assembly Model

Mitotic error correction model

Mitotic error correction model

Brownian Dynamics Tumor Simulator

Brownian Dynamics Tumor Simulator

SARS-CoV-2 Biophysical Model

SARS-CoV-2 Biophysical Model

Biophysical Tubulin Dynamics Model

Biophysical Tubulin Dynamics Model

Software

Image Processing Tools

+ TipTracker Code.

TipTracker Code.

+ FlowTrack Code

FlowTrack Code

+ BeadTrack Code

BeadTrack Code

+ Model Convolution Plugin

Model Convolution Plugin

Stochastic Simulations of Cellular Processes

+ Cell Migration Simulator, version 1.0 (CMSv1.0)

Cell Migration Simulator, version 1.0 (CMSv1.0)

Reference publications

+ Motor-Clutch Model for Cell Traction

Motor-Clutch Model for Cell Traction

+ Mechanochemical Microtubule Assembly Model

Mechanochemical Microtubule Assembly Model

+ Mitotic error correction model

Mitotic error correction model

+ Brownian Dynamics Tumor Simulator

Brownian Dynamics Tumor Simulator

+ SARS-CoV-2 Biophysical Model

SARS-CoV-2 Biophysical Model

+ Biophysical Tubulin Dynamics Model

Biophysical Tubulin Dynamics Model

TipTracker Code.

FlowTrack Code

BeadTrack Code

Model Convolution Plugin

Cell Migration Simulator, version 1.0 (CMSv1.0)

Motor-Clutch Model for Cell Traction

Mechanochemical Microtubule Assembly Model

Mitotic error correction model

Brownian Dynamics Tumor Simulator

SARS-CoV-2 Biophysical Model

Biophysical Tubulin Dynamics Model