Biodiversity Information Science and Standards : Conference Abstract
Conference Abstract
Measuring Morphological Functional Leaf Traits From Digitized Herbarium Specimens Using TraitEx Software
expand article infoJitendra Gaikwad‡,§, Abdelaziz Triki|, Bassem Bouaziz|
‡ Friedrich Schiller University Jena, Jena, Germany
§ German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| MIRACL/CRNS-University of Sfax, Sfax, Tunisia
Open Access


Herbarium specimens are of vital importance for understanding biodiversity. There are more than 350 million specimens stored in herbaria worldwide (Thiers 2018) Globally, many herbaria have undertaken digitization projects of plant specimens, on a massive scale, to preserve them and to make the images easily accessible to users.

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 ( are making efforts to fill the gaps in the observed trait matrix (Schrodt et al. 2015). In order to complement the global efforts, we have developed a software tool, TraitEx , which can measure quantitative traits such as the length, area, width and perimeter of leaves along with the petiole length from digitized herbarium specimens.

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 ( 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 The tool is made available under the BSD-2-Clause License.


TraitEx, leaf traits, digitized specimens, herbarium, functional traits

Presenting author

Jitendra Gaikwad

Presented at

Biodiversity_Next 2019


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


Grant title

MAMUDS: Management of Multimedia Data for Science (BMBF Project No. 01D16009)

Hosting institution

Friedrich Schiller University Jena, Germany


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