Programs

© K.T. Haas. FEM model of Pavement cells' lobe formation

Expanding beam model using FEM

Program can be downloaded from my GitHub or Zenodo page:

This repository contains Matlab based implementation of the 'expanding beam' model using a 3D nonlinear FEM approach to describe growth and morphogenesis of the pavement cells.

Grafeo - program for the single-molecule localization microscopy data anlysis

Program can be downloaded from my GitHub or Zenodo page:

Grafeo is Matlab based program for the analysis of single-molecule localization microscopy (SMLM) data e.g., dSTORM or PALM. It works on a single molecule coordinates rather than pixelated images. Grafeo uses various pointillist approaches previously described in the literature, e.g., Voronoi Tessellation, Delaunay Triangulation, Ripley's function. The first Grafeo version (1.beta) was published in Haas et al., 'Single-molecule localization microscopy reveals molecular transactions during RAD51 filament assembly at cellular DNA damage sites', Nucleic Acids Research, 2018,gkx1303, https://doi.org/10.1093/nar/gkx1303. Grafeo is continuously updated. The current Grafeo version is Grafeo v2.1.à It has new functionalities, developed for the article: Pectin homogalacturonan nanofilament expansion drives morphogenesis in plant epidermal cells, Haas et al., Science 2020, DOI: 10.1126/science.aaz5103. This includes the support for the three-colors data files, possibility to upload Nikon multicolor molecular list files, load Vutara data in '.mat' format, calculate graphs, and Ripley's function for small ROI, create different types of ROI, visualize the Z position using colormaps.

© K.T. Haas. (Left) The 3D dSTORM data scatterplot of radiation-induced focus imaged in the Hela cell nucleus. (Right) The same data represented using Delauney Triangulation. Violet - RAD51, Green - RPA. Data vizualised with Grafeo.

Shape Spectra Analysis

Program can be downloaded from my GitHub or Zenodo page:

Matlab scripts to analyse cell shape using a Fourier Transform and to sonify the cellular outlines.

© K.T. Haas. From left to right. (1) The contour of growing pavement cells at three successive days. (2) Contour represented as radius, the distance from the cell center to the cell periphery. (3) The shape spectra is a Fourier Transform of a radius. (4) Each normalized frequency can be represented as the number of equal-length segments dividing cellular outline.