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Biodiversity Information Science and Standards : Conference Abstract
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Jitendra Gaikwad‡,§, Abdelaziz Triki|, Bassem Bouaziz|
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Corresponding author: Jitendra Gaikwad (jitendra.gaikwad@uni-jena.de)
Received: 11 Jun 2019 | Published: 13 Jun 2019
© 2019 Jitendra Gaikwad, Abdelaziz Triki, Bassem Bouaziz
This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Citation: Gaikwad J, Triki A, Bouaziz B (2019) Measuring Morphological Functional Leaf Traits From Digitized Herbarium Specimens Using TraitEx Software. Biodiversity Information Science and Standards 3: e37091. https://doi.org/10.3897/biss.3.37091
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Abstract
Herbarium specimens are of vital importance for understanding biodiversity. There are more than 350 million specimens stored in herbaria worldwide (
Over the past years, with significant advances in the field of computer vision, new potential uses of digitized specimens have emerged, such as automated species identification using qualitative morphological traits. However, due to lack of efficient tools, efforts to extract functional (quantitative) morphological traits from digitized herbarium specimens are lagging behind. Functional trait data is of significant importance to understand the functioning of the ecosystem and interactions between biotic and abiotic factors. It is currently fragmented and initiatives such as TRY Trait database (https://www.try-db.org) are making efforts to fill the gaps in the observed trait matrix (
TraitEx is a standalone Java-based open source tool developed after extensive interactions with biodiversity researchers. The main features of the tool are: (1) efficiently handling high-resolution specimen images, (2) accurately extracting measurements from specimens with varied leaf shapes that are mounted using white tape, (3) integrating ImageJ functionality (https://imagej.net/Welcome) to pre-process and edit the images, (4) measuring trait values to export in comma separated values (CSV) format along with original image and (5) reducing potential damage of fragile specimens, which might occur while physically measuring the traits.
Along with user guide and documentation, TraitEx tool is available at https://bitbucket.org/traitExTool/traitextool. The tool is made available under the BSD-2-Clause License.
Keywords
TraitEx, leaf traits, digitized specimens, herbarium, functional traits
Presenting author
Jitendra Gaikwad
Presented at
Biodiversity_Next 2019
Acknowledgements
1. Prof. Birgitta König-Ries, Friedrich Schiller University Jena, Germany.
2. Prof. Faeiz Gargouri, University of Sfax, Tunisia.
3. Prof. Frank Hellwig, Herbarium Haussknecht, Friedrich Schiller University Jena, Germany.
4. Dr. Jens Kattge, Max Planck Institute for Biogeochemistry, Jena, Germany.
5. Dr. Joern Hetschel, Herbarium Haussknecht, Friedrich Schiller University Jena, Germany.
6. Mr. Hamed Hamdi, Friedrich Schiller University Jena, Germany.
7. Mr. Martin Hohmuth, Friedrich Schiller University Jena, Germany.
8. Dr. Jana Dümmler, Servicezentrum Forschung und Transfer, Friedrich Schiller University Jena, Germany.
9. Dr. Susanne Tautenhahn, Max Planck Institute for Biogeochemistry, Jena, Germany.
Funding program
STC-TUNGER-2015
Grant title
MAMUDS: Management of Multimedia Data for Science (BMBF Project No. 01D16009)
Hosting institution
Friedrich Schiller University Jena, Germany
References
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BHPMF - a hierarchical Bayesian approach to gap-filling and trait prediction for macroecology and functional biogeography.Global Ecology and Biogeography24(12):1510‑1521. https://doi.org/10.1111/geb.12335
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[continuously updated]. Index Herbariorum: A global directory of public herbaria and associated staff. New York Botanical Garden's Virtual Herbarium. http://sweetgum.nybg.org/science/ih