Related Experiment Video
Updated: Aug 24, 2026
LeafJ: An ImageJ Plugin for Semi-automated Leaf Shape Measurement
Published on: January 21, 2013
Garryanalyzer: A morphometric workflow and open-source ImageJ plug-in for quantitative morphological analysis of
Ziqi Xie1,2, Tan Bahar1, Keith Karoly1
1Biology Department Reed College Portland 97202 Oregon USA.
Premise:
Accurate species identification is crucial for ecological restoration and can be especially challenging for understudied non-model species. Quercus garryana is the only native oak species in the Pacific Northwest and is an important component of the endangered oak savanna ecosystem. Quercus robur is an imported ornamental species from Europe and has been found to be mistakenly planted as Q. garryana in habitat restoration projects.
Methods:
We measured leaf morphological traits sampled from herbarium collections in their native ranges using the digital morphometric tools MorphoLeaf and Tomato Analyzer. We then used Lasso logistic analysis to generate a predictive model and tested it on leaves from Portland, Oregon. To streamline this species detection process, we developed Garryanalyzer, an ImageJ plug-in that automatically measures leaf traits and outputs species predictions.
Results:
Garryanalyzer demonstrated 95% accuracy in predicting the species identity of herbarium specimens of oaks. Garryanalyzer correctly identified all Q. robur individuals sampled in Portland but showed lower accuracy for Q. garryana.
Discussion:
Many existing morphometric software are not open source, which makes them unable to be customized to specific study systems. Garryanalyzer is built upon the widely used open-source ImageJ platform. This study also demonstrates a viable workflow for developing similar tools for other ecologically important non-model plant species.
