L Dupuy et al.
Scottish Crop Research Institute
Plants are the ideal models for the engineering of synthetic multicellular systems, however there is a need for tools to measure, process and design such systems.
Quantitative analysis of plant multicellular kinematics. The segment cell architectures approach: grow a region of pixels incrementally by raising the intensity of the pixels. The basin (a set of pixels) are initiated at cell centers, and expand when neighbors have a lower intensity. The balloon approach: ballons are initiated at cell centres, there is contact search initialization, and then "physical" inflation of balloons under certain circumstances. What is the application to cell growth kinematics? You can find really clear geometric rules which drive where/when the cell divisions occur.
Integrating molecular and computational tools. Automated analysis of cell growth involves labelling plasma membrane and nucleus simultaneously, which allows combining algorithms, automation of cell search, and facilitates 3d segmentation. Standardization of biological parts on a cell basis includes normalizing gene expression; there is also a ImageJ plugin for automation of ratiometric analyses; and more.
Computational models for tissue growth and development. There are computational tools and molecular tools that can help out. Modelling tissue growth is a multiscale problem. You also have to take into account the mechanics of growth, such as: cells are closed-walled structures maintained in tension by turgor pressure; permanent deformation of cell wall material enables cell expansion; the cell genetic activity influences the cell wall material properties. CellModeller is a tool for data analysis, visualisation, simulation, and segmentation reconstruction. It uses an XML exchange format, a Python interface, and a data structure described in C++. He then described how CellModeller works by giving a trichome pattern system example. Trichomes are root hairs that form on the root. The pattern of these types of cells are not random.
Multicellularity is key for building complexity of a system. Plant systems are ideal for engineering cell-cell interactions. There is a whole group of tools to create models, from bytes to molecules.
Personal Comment: These notes are a bit scattered, as it was just after I gave my talk, and I wasn't completely in zen note-taking mode However, there were some great pictures of plant cells and models, and it was a well-structured talk. It was nice to see modelling tools for multiple cells.
Please note that this post is merely my notes on the presentation. They are not guaranteed to be correct, and unless explicitly stated are not my opinions. They do not reflect the opinions of my employers. Any errors you can happily assume to be mine and no-one else's. I'm happy to correct any errors you may spot – just let me know!