CuticleTrace: A toolkit for capturing cell outlines from leaf cuticle with implications for paleoecology and paleoclimatology

Benjamin A. Lloyd, Richard S. Barclay, Regan E. Dunn, Ellen D. Currano, Ayuni I. Mohamaad, Kymbre Skersies, Surangi W. Punyasena

Research output: Contribution to journalArticlepeer-review


Premise: Leaf epidermal cell morphology is closely tied to the evolutionary history of plants and their growth environments and is therefore of interest to many plant biologists. However, cell measurement can be time consuming and restrictive with current methods. CuticleTrace is a suite of Fiji and R-based functions that streamlines and automates the segmentation and measurement of epidermal pavement cells across a wide range of cell morphologies and image qualities. Methods and Results: We evaluated CuticleTrace-generated measurements against those from alternate automated methods and expert and undergraduate hand tracings across a taxonomically diverse 50-image data set of variable image qualities. We observed ~93% statistical agreement between CuticleTrace and expert hand-traced measurements, outperforming alternate methods. Conclusions: CuticleTrace is a broadly applicable, modular, and customizable tool that integrates data visualization and cell shape measurement with image segmentation, lowering the barrier to high-throughput studies of epidermal morphology by vastly decreasing the labor investment required to generate high-quality cell shape data sets.

Original languageEnglish (US)
Article numbere11566
JournalApplications in Plant Sciences
Issue number1
StatePublished - Jan 1 2024


  • cell shape
  • high-throughput phenotyping
  • image processing
  • image segmentation
  • leaf area index
  • leaf epidermis
  • paleobotany
  • paleoecology

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Plant Science


Dive into the research topics of 'CuticleTrace: A toolkit for capturing cell outlines from leaf cuticle with implications for paleoecology and paleoclimatology'. Together they form a unique fingerprint.

Cite this