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Convert a raw AXIOScan dataset in CZI format to Zarr ready for stitching

This module can be used for single on multiple vm's creation in vShpere

Data and code for the paper under preparation :

Rational design of a sampling protocol for detection of a subcellular pathogen to demonstrate area freedom

Authors: D.B. Bonnéry, L.Pretorius, A.E.C. Jooste, A. Geering, C.A. Gilligan

Scripts and software related to Bhatia, Åhl, Jönsson and Heisler "Quantitative analysis of auxin sensing in leaf primordia argues against proposed role in regulating leaf dorsoventrality"

Scripts and software connected to the publication Meyer, Teles, Formosa-Jordan et al (2017) "Fluctuations of the transcription factor ATML1 generate the pattern of giant cells in the Arabidopsis sepal"

Files needed to run models for Bou Daher et al (2018) 'Anisotropic growth is achieved through the additive mechanical effect of material anisotropy and elastic asymmetry' eLife

Code for simulations of individual Microtubules in 3D and constrained by a meshed description of a cell membrane.

Scripts and software connected to the publication Landrein et al (2018) "Nitrate modulates stem cell dynamics in Arabidopsis shoot meristems through cytokinins"

Repository for the software described in Robert, Jönsson and Meyer-Hermann (2018) "MoonFit, a minimal interface for fitting ODE dynamical models, bridging simulation by experimentalists and customization by C++ programmers"

Model files for simulations in the publication Caggiano et al (2017) "Cell type boundaries organize plant development"

Scripts and software for generating the results of Korsbo and Jönsson (2020) "It’s about time: Analysing simplifying assumptions for modelling multi-step pathways in systems biology"

Scripts related to the manuscript "Cytoskeletal organization in isolated plant cells under geometry control".

Organism model files for creating budding yeast simulations as presented in the paper "An explicit spatial model of yeast microcolony growth".

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

MATLAB code for running the simulations for the paper "Auxin transport model for leaf venation".

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