title: Semi-automated 3D leaf reconstruction and analysis of trichome patterning from light microscopic images.
abstract: Trichomes are leaf hairs that are formed by single cells on the leaf surface. They are known to be involved in pathogen resistance. Their patterning is considered to emerge from a field of initially equivalent cells through the action of a gene regulatory network involving trichome fate promoting and inhibiting factors. For a quantitative analysis of single and double mutants or the phenotypic variation of patterns in different ecotypes, it is imperative to statistically evaluate the pattern reliably on a large number of leaves. Here we present a method that enables the analysis of trichome patterns at early developmental leaf stages and the automatic analysis of various spatial parameters. We focus on the most challenging young leaf stages that require the analysis in three dimensions, as the leaves are typically not flat. Our software TrichEratops reconstructs 3D surface models from 2D stacks of conventional light-microscope pictures. It allows the GUI-based annotation of different stages of trichome development, which can be analyzed with respect to their spatial distribution to capture trichome patterning events. We show that 3D modeling removes biases of simpler 2D models and that novel trichome patterning features increase the sensitivity for inter-accession comparisons.
authors: Max Planck Institute for Plant Breeding Research, Cologne, Germany.
authors: Henrik
authors: H
authors: Failmezger
authors: Benjamin
authors: B
authors: Jaegle
authors: Andrea
authors: A
authors: Schrader
authors: Martin
authors: M
authors: Hülskamp
authors: Achim
authors: A
authors: Tresch
mesh_terms: D017360:Arabidopsis / Q000254:growth & development; D029681:Arabidopsis Proteins / Q000378:metabolism; D001331:Automation; D002454:Cell Differentiation; D019295:Computational Biology / Q000379:methods*; D003196:Computer Graphics; D017343:Genes, Plant; D007091:Image Processing, Computer-Assisted / Q000379:methods; D021621:Imaging, Three-Dimensional / Q000379:methods*; D009154:Mutation; D010641:Phenotype; D019441:Plant Epidermis / Q000254:growth & development; D018515:Plant Leaves / Q000254:growth & development*; D012984:Software; D064201:Trichomes / Q000254:growth & development*
chemical_list: D029681:Arabidopsis Proteins
references: Cell. 1994 Feb 11;76(3):555-66
references: 8313475
references: Plant Cell. 2006 Sep;18(9):2145-56
references: 16905654
references: Int Rev Cell Mol Biol. 2011;286:67-106
references: 21199780
references: IEEE Trans Image Process. 2008 Jul;17(7):1144-53
references: 18586622
references: EMBO J. 2002 Oct 1;21(19):5036-46
references: 12356720
references: Development. 1998 Apr;125(7):1161-71
references: 9477315
references: Dev Cell. 2012 Jan 17;22(1):64-78
references: 22227310
references: Micron. 2001 Aug;32(6):559-69
references: 11166576
references: Microsc Res Tech. 2004 Sep;65(1-2):33-42
references: 15570586
references: Curr Opin Plant Biol. 2009 Oct;12(5):587-92
references: 19783469
references: Med Image Anal. 2001 Dec;5(4):281-99
references: 11731307
references: IET Syst Biol. 2012 Aug;6(4):143-53
references: 23039695
references: Microsc Res Tech. 2012 Nov;75(11):1582-92
references: 22972756
references: Development. 2005 Dec;132(24):5387-98
references: 16291794
references: Curr Top Dev Biol. 2010;91:299-321
references: 20705186
references: Development. 2011 Nov;138(22):5039-48
references: 22028035
references: Plant Cell. 1994 Aug;6(8):1065-1076
references: 12244266
references: Plant J. 2008 Nov;56(3):470-82
references: 18643999