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This is mirroring the audapter_mex repo for Abbie

Scripts to run the models presented in the PLoS Comp Biol paper "Stress and Strain Provide Positional and Directional Cues in Development".

Files to generate simulations results for the paper "A continuous growth model for plant tissue".

Segmentation tool allowing finding nuclei in 3D and cells via membranes in 2D.

companion code for "The Discriminative Kalman Filter for Bayesian Filtering with Nonlinear and Nongaussian Observation Models"

These slides were presented at my dissertation defense (Division of Applied Mathematics, Brown University, 23 May 2018).

This repository contains code implementations for the Discriminative Kalman Filter.

Scripts used for the manuscript "Tissue folding at the organ-meristem boundary results in nuclear compression and chromatin compaction"

An unsupervised segmentation and edge detection hybrid algorithm for PLIF images.

Scripts and instructions on how to reproduce the work described in Gibson, Jönsson, Spelman (2024) "Mean-field theory approach to three-dimensional nematic phase transitions in microtubules"

Project code for Gould et al., 2018, "Coordination of robust single cell rhythms in the Arabidopsis circadian clock".

Project data and code for Greenwood et al., 2019, "Coordinated circadian timing through the integration of local inputs in Arabidopsis thaliana".

Project code for Greenwood et al., "A spatial model of the plant circadian clock reveals design principles for coordinated timing".

Francois's MATLAB code

Odds and ends that may be of use...

Stochastic pulsing of gene expression enables the generation of spatial patterns in Bacillus subtilis biofilms

adjustments to robust_correlation_toolbox to ensure alpha = 0.05 across all sample sizes.