MorphoGraphX: A platform for quantifying morphogenesis in 4D

TLDR

Morphogenesis arises from complex multiscale genetic and mechanical interactions, yet quantifying it is difficult because full 3D analysis is computationally expensive and 2D projections introduce geometric artifacts on curved organs. The study aims to quantify cell shape, proliferation, and gene expression during morphogenesis by introducing MorphoGraphX, a tool that analyzes curved surface images directly from 3D data. MorphoGraphX operates on curved surface images extracted from 3D data, providing algorithms for cell segmentation, lineage tracking, fluorescence quantification, and a modular design that allows integration of existing libraries or new algorithms. Using MorphoGraphX, extracted cell geometries can be exported as templates for simulation models, enabling investigation of shape–gene–growth interactions.

Abstract

Morphogenesis emerges from complex multiscale interactions between genetic and mechanical processes. To understand these processes, the evolution of cell shape, proliferation and gene expression must be quantified. This quantification is usually performed either in full 3D, which is computationally expensive and technically challenging, or on 2D planar projections, which introduces geometrical artifacts on highly curved organs. Here we present MorphoGraphX (www.MorphoGraphX.org), a software that bridges this gap by working directly with curved surface images extracted from 3D data. In addition to traditional 3D image analysis, we have developed algorithms to operate on curved surfaces, such as cell segmentation, lineage tracking and fluorescence signal quantification. The software's modular design makes it easy to include existing libraries, or to implement new algorithms. Cell geometries extracted with MorphoGraphX can be exported and used as templates for simulation models, providing a powerful platform to investigate the interactions between shape, genes and growth.