Related Tools and Frameworks
Numerous tools and frameworks have been developed for morphometrics. Here, we provide a brief overview of some notable examples that illustrate the diversity of approaches in this field.
This section is subject to updates as new tools become available. Suggestions or corrections are always welcome.
Software and Tools
General or Framework-Level Tools
| Tool | Language / Type | Note |
|---|---|---|
| ImageJ (Schneider, Rasband, and Eliceiri 2012) / Fiji (Schindelin et al. 2012) |
JAVA / GUI | |
| LAMINA (Bylesjö et al. 2008) | Standalone GUI | |
| napari (Sofroniew et al. 2025) | Python / GUI | Interactive viewer in Python |
Outline-Based Tools
| Tool | Language / Type | Note |
|---|---|---|
| SHAPE (Iwata 2002) | Windows GUI | Classic EFD analysis software. |
| Momocs (Bonhomme et al. 2014) | R package | Comprehensive outline & landmark morphometrics. |
| Ellishape (Wu et al. 2024) | Python CLI / GUI (standalone and web) | True normalization of EFDs. |
| PyEFD | Python library | Lightweight implementation of elliptic Fourier descriptors. |
| LeafMachine (Weaver, Ng, and Laport 2020) | Python / GUI | Automatic leaf segmentation and classification. |
| LeafMachine2 (Weaver and Smith 2023) | Python / GUI | Automated extraction of leaf and plant trait data from digital herbarium images using machine learning and computer vision. |
| MorphoLeaf (Biot et al. 2016) | R / C++ hybrid | Leaf contour extraction and shape quantification. |
| LeafJ (Maloof et al. 2013) | ImageJ plugin | Batch leaf outline extraction. |
| DiaOutline (Wishkerman and Hamilton 2018) | GUI / R |
Landmark-Based Tools
| Tool | Language / Type | Note |
|---|---|---|
| Morphological Analysis of Size and Shape (MASS) (Chuanromanee, Cohen, and Ryan 2019) | MATLAB | Morphological Analysis of Size and Shape. |
| TPS Series (Rohlf 2015) | Windows GUI | Classic geometric morphometric suite. |
| geomorph (Adams and Otárola-Castillo 2013) | R package | Landmark-based morphometric analysis. |
| MorphoJ (Klingenberg 2011) | Java GUI | Widely used for landmark-based morphometrics. |
| shapes (Dryden 2025) | R package | Statistical analysis of landmark shapes in R |
Other Specialized Tools
| Tool | Language / Type | Note |
|---|---|---|
| LEAF GUI (Price et al. 2011) | MATLAB / GUI | Software quantifing leaf vein networks. As of 2025, the download link seems to be no longer available. |
| LeafProcessor (Backhaus et al. 2010) | C/C++ and MATLAB / Script file | Automatically identify plant species or genotypes. Although the paper mentions that a standalone program would be distributed, only a MATLAB (.m) file appears to be available. |
References
Adams, Dean C., and Erik Otárola-Castillo. 2013. “Geomorph: An r Package for the Collection and Analysis of Geometric Morphometric Shape Data.” Methods in Ecology and Evolution 4 (4): 393–99. https://doi.org/10.1111/2041-210X.12035.
Backhaus, Andreas, Asuka Kuwabara, Marion Bauch, Nick Monk, Guido Sanguinetti, and Andrew Fleming. 2010. “Leafprocessor: A New Leaf Phenotyping Tool Using Contour Bending Energy and Shape Cluster Analysis.” New Phytologist 187 (1): 251–61. https://doi.org/10.1111/j.1469-8137.2010.03266.x.
Biot, Eric, Millán Cortizo, Jasmine Burguet, Annamaria Kiss, Mohamed Oughou, Aude Maugarny-Calès, Beatriz Gonçalves, et al. 2016. “Multiscale Quantification of Morphodynamics: MorphoLeaf Software for 2D Shape Analysis.” Development 143 (18): 3417–28. https://doi.org/10.1242/dev.134619.
Bonhomme, Vincent, Sandrine Picq, Cédric Gaucherel, and Julien Claude. 2014. “Momocs : Outline Analysis Using R.” Journal of Statistical Software 56 (13). https://doi.org/10.18637/jss.v056.i13.
Bylesjö, Max, Vincent Segura, Raju Y. Soolanayakanahally, Anne M. Rae, Johan Trygg, Petter Gustafsson, Stefan Jansson, and Nathaniel R. Street. 2008. “LAMINA: A Tool for Rapid Quantification of Leaf Size and Shape Parameters.” BMC Plant Biology 8 (1): 82. https://doi.org/10.1186/1471-2229-8-82.
Chuanromanee, Tya S., James I. Cohen, and Gillian L. Ryan. 2019. “Morphological Analysis of Size and Shape ( MASS ): An Integrative Software Program for Morphometric Analyses of Leaves.” Applications in Plant Sciences 7 (9): e11288. https://doi.org/10.1002/aps3.11288.
Dryden, Ian. 2025. Shapes: Statistical Shape Analysis. https://github.com/iandryden/shapes.
Iwata, H. 2002. “SHAPE: A Computer Program Package for Quantitative Evaluation of Biological Shapes Based on Elliptic Fourier Descriptors.” Journal of Heredity 93 (5): 384–85. https://doi.org/10.1093/jhered/93.5.384.
Klingenberg, Christian Peter. 2011. “Morpho J: An Integrated Software Package for Geometric Morphometrics.” Molecular Ecology Resources 11 (2): 353–57. https://doi.org/10.1111/j.1755-0998.2010.02924.x.
Maloof, Julin N., Kazunari Nozue, Maxwell R. Mumbach, and Christine M. Palmer. 2013. “LeafJ: An ImageJ Plugin for Semi-Automated Leaf Shape Measurement.” Journal of Visualized Experiments (JoVE), no. 71 (January): e50028. https://doi.org/10.3791/50028.
Price, Charles A., Olga Symonova, Yuriy Mileyko, Troy Hilley, and Joshua S. Weitz. 2011. “Leaf Extraction and Analysis Framework Graphical User Interface: Segmenting and Analyzing the Structure of Leaf Veins and Areoles.” Plant Physiology 155 (1): 236–45. https://doi.org/10.1104/pp.110.162834.
Rohlf, F. James. 2015. “The Tps Series of Software.” Hystrix, the Italian Journal of Mammalogy 26 (1): 9–12. https://doi.org/10.4404/hystrix-26.1-11264.
Schindelin, Johannes, Ignacio Arganda-Carreras, Erwin Frise, Verena Kaynig, Mark Longair, Tobias Pietzsch, Stephan Preibisch, et al. 2012. “Fiji: An Open-Source Platform for Biological-Image Analysis.” Nature Methods 9 (7): 676–82. https://doi.org/10.1038/nmeth.2019.
Schneider, Caroline A., Wayne S. Rasband, and Kevin W. Eliceiri. 2012. “NIH Image to ImageJ: 25 Years of Image Analysis.” Nature Methods 9 (7): 671–75. https://doi.org/10.1038/nmeth.2089.
Sofroniew, Nicholas, Talley Lambert, Grzegorz Bokota, Juan Nunez-Iglesias, Peter Sobolewski, Andrew Sweet, Lorenzo Gaifas, et al. 2025. Napari: A Multi-Dimensional Image Viewer for Python. Zenodo. https://zenodo.org/doi/10.5281/zenodo.17367124.
Weaver, William N., Julienne Ng, and Robert G. Laport. 2020. “LeafMachine: Using Machine Learning to Automate Leaf Trait Extraction from Digitized Herbarium Specimens.” Applications in Plant Sciences 8 (6): e11367. https://doi.org/10.1002/aps3.11367.
Weaver, William N., and Stephen A. Smith. 2023. “From Leaves to Labels: Building Modular Machine Learning Networks for Rapid Herbarium Specimen Analysis with LeafMachine2.” Applications in Plant Sciences 11 (5): e11548. https://doi.org/10.1002/aps3.11548.
Wishkerman, Asher, and Paul B. Hamilton. 2018. “Shape Outline Extraction Software (DiaOutline) for Elliptic Fourier Analysis Application in Morphometric Studies.” Applications in Plant Sciences 6 (12): e01204. https://doi.org/10.1002/aps3.1204.
Wu, Hui, Jia-Jie Yang, Chao-Qun Li, Jin-Hua Ran, Ren-Hua Peng, and Xiao-Quan Wang. 2024. “Reliable and Superior Elliptic Fourier Descriptor Normalization and Its Application Software ElliShape with Efficient Image Processing.” https://arxiv.org/abs/2412.10795.