title: LeafJ: an ImageJ plugin for semi-automated leaf shape measurement.
abstract: High throughput phenotyping (phenomics) is a powerful tool for linking genes to their functions (see review and recent examples). Leaves are the primary photosynthetic organ, and their size and shape vary developmentally and environmentally within a plant. For these reasons studies on leaf morphology require measurement of multiple parameters from numerous leaves, which is best done by semi-automated phenomics tools. Canopy shade is an important environmental cue that affects plant architecture and life history; the suite of responses is collectively called the shade avoidance syndrome (SAS). Among SAS responses, shade induced leaf petiole elongation and changes in blade area are particularly useful as indices. To date, leaf shape programs (e.g. SHAPE, LAMINA, LeafAnalyzer, LEAFPROCESSOR) can measure leaf outlines and categorize leaf shapes, but can not output petiole length. Lack of large-scale measurement systems of leaf petioles has inhibited phenomics approaches to SAS research. In this paper, we describe a newly developed ImageJ plugin, called LeafJ, which can rapidly measure petiole length and leaf blade parameters of the model plant Arabidopsis thaliana. For the occasional leaf that required manual correction of the petiole/leaf blade boundary we used a touch-screen tablet. Further, leaf cell shape and leaf cell numbers are important determinants of leaf size. Separate from LeafJ we also present a protocol for using a touch-screen tablet for measuring cell shape, area, and size. Our leaf trait measurement system is not limited to shade-avoidance research and will accelerate leaf phenotyping of many mutants and screening plants by leaf phenotyping.
authors: Department of Plant Biology, University of California Davis, USA. jnmaloof@ucdavis.edu
authors: Julin N
authors: JN
authors: Maloof
authors: Kazunari
authors: K
authors: Nozue
authors: Maxwell R
authors: MR
authors: Mumbach
authors: Christine M
authors: CM
authors: Palmer
mesh_terms: D017360:Arabidopsis / Q000033:anatomy & histology* / Q000235:genetics / Q000378:metabolism; D007091:Image Processing, Computer-Assisted / Q000379:methods*; D010788:Photosynthesis; D018515:Plant Leaves / Q000033:anatomy & histology* / Q000235:genetics / Q000378:metabolism; D012984:Software
references: Plant Physiol. 2012 Mar;158(3):1230-40
references: 22247269
references: J Plant Res. 2006 Jan;119(1):37-42
references: 16284709
references: Nat Methods. 2011 Jun 12;8(7):599-605
references: 21666667
references: BMC Plant Biol. 2008 Jul 22;8:82
references: 18647399
references: Plant J. 2006 Nov;48(4):638-44
references: 17076802
references: Trends Plant Sci. 2011 Dec;16(12):635-44
references: 22074787
references: PLoS One. 2012;7(1):e29570
references: 22253737
references: New Phytol. 2011 Jan;189(1):122-34
references: 20854397
references: J Hered. 2002 Sep-Oct;93(5):384-5
references: 12547931
references: New Phytol. 2010 Jul;187(1):251-261
references: 20456045
references: J Exp Bot. 2010 Aug;61(13):3519-28
references: 20660495
references: Plant J. 2008 Feb;53(3):578-86
references: 18028263
references: Annu Rev Plant Biol. 2006;57:477-96
references: 16669771
references: Arabidopsis Book. 2012;10:e0157
references: 22582029
references: G3 (Bethesda). 2012 Jan;2(1):29-34
references: 22384379