Richard S. Smith - Quantifying morphogenesis with MorphoGraphX

  • Date: Jun 29, 2016
  • Time: 02:00 PM - 03:30 PM (Local Time Germany)
  • Speaker: Richard S. Smith
  • Location: Central Building
  • Room: Seminar Room
  • Host: Arun Sampathkumar
Morphogenesis emerges from complex interactions between genetic and mechanical processes. Computer simulation models are becoming increasingly important to aid our understanding of the complexity involved, in an emerging field that is now being called Computational Morphodynamics. Key to this methodology is the combination of experimental work with dynamic, spatial simulation modeling. In order to analyze shape change in developing organs, it is essential to be able to quantify cell shape and gene expression changes at cellular resolution, over multiple time points. Ideally, a full 3D quantification of shape change and gene reporter expression over time is desired. Unfortunately, this is often technically challenging. In cases where the processes of interest occur on a surface layer of cells, 2D (i.e. max) projections can be used. However on highly curved organs and tissues, flat projections can introduce too much distortion to accurately record cell shape change. Here I will present a new image processing software called MorphoGraphX that bridges this gap by working directly with curved surface images extracted from 3D data. After recognizing the shape of a 3D sample, the surface is extracted and the signal is projected on the surface to form a curved “2.5D” image. I will demonstrate many of the tools we have developed to enable image processing on these 2.5D images, and how to use them to quantify 4D confocal time-lapse data sets. Finally, I will present our inroads towards developing an integrated simulation and imaging environment for Computational Morphodynamics.
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