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TraitEx: tool for measuring morphological functional traits from digitized herbarium specimens

Title: TraitEx: tool for measuring morphological functional traits from digitized herbarium specimens
Authors: Jitendra Gaikwad, Abdelaziz Triki, Bassem Bouaziz, Hamdi Hamed, Jörn Hentschel
Source: https://icei2018.uni-jena.de/
Place: Jena, Germany
Date: 2018-12-18
Type: Demo
Abstract:

Functional trait data is of significant importance to understand how species respond to biotic and abiotic factors. However, despite several global efforts, functional trait data is largely fragmented and available in heterogeneous formats. Initiatives such as TRY (https://www.try-db.org), which is a global network of vegetation scientists, are making efforts by applying novel methods in machine learning to fill gaps in the observed trait matrix and predict plant traits at continental to global scale. To complement existing efforts and increase plant trait data, within the Managing Multimedia Data for Science (MAMUDS) project, we have developed a software tool TraitEx to measure functional traits such as length, width, area and size of leaves from the digitized type specimens stored in herbarium Haussknecht (http://www.spezbot.uni-jena.de/herbarium/). To preserve specimens and make associated information easily accessible to researchers and public, herbarium Haussknecht from Germany, have digitized more than 30000 type specimens. TraitEx is a semi-automatic and open source tool, developed using computer programming language Java. The main features of TraitEx are (1) ability to handle high resolution specimen images, (2) supports extraction of trait measurements from multiple and diverse leaf shapes, (3) efficiently extract measurements from leaves of specimens that are mounted using white tapes, (3) ImageJ functions integrated for pre-processing and editing of images, (4) functionality to export measured values in CSV format along with original image, thumbnail and coordinates of the measured leaves, (5) user-friendly viewer to visualize measured leaves and values and (6) facilitates easy and quick measurement of leaf traits with high accuracy as compared to manual measurements process. As part of the demo we will (1) introduce TraitEx and use digitized type specimens from herbarium Haussknecht to show the processes involved in extraction of morphological trait extraction, (2) show how to download and install TraitEx if user want to try on their laptops and (3) document user experience as feedback. 

URL: https://doi.org/10.22032/dbt.37846