I’m happy to say that Springer just published a book entitled “Plant Hormones, methods and protocols”, for which I’m a coauthor of the chapter “In Silico Methods for Cell Annotation, Quantification of Gene Expression, and Cell Geometry at Single-Cell Resolution Using 3DCellAtlas”. In it, we describe how to use our plugin 3DCellAtlas for the open source software MorphoGraphX, a tool to identify cell type and position within topologically cylindrical plant organs, and simultaneously quantify 3D cell anisotropy and reporter abundance at single-cell resolution. 3DCellAtlas is able to generate digital single-cell cellular atlases of plant organs, and so enables 3D cell geometry and reporter abundance (gene/protein/biosensor) from multiple samples to be integrated at single-cell resolution across whole organs. The original paper describing the work can be found here.

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