Scanning Tiny Data Matrix Codes for Naturalis ARISE Biodiversity Sampling

Introduction

Naturalis ARISE has a bold mandate: to completely map multicellular diversity in the Netherlands. That means building a national DNA database of everything from butterflies to tiny soil Fungi - 40,000 plants, animals and fungi in total. It may sound like an audacious goal, but it is very achievable with new technologies such as mobile phones and barcode scanning.

Challenge

The ARISE consortium has a network of 150 scientific experts who are committed to collecting specimens, identifying the species, logging the date and location, then mailing them in, much as you would for a home DNA test.

Inside the testing kit are test tubes, plastic bag and a tiny slip of paper printed with a 1cm square Data Matrix code, which gives a unique identifier to each specimen collected. Collectors log each specimen in the ARISE web app on their phones, identifying the species, location and time collected. The Data Matrix code is scanned and then added to the test tube of alcohol along with the specimen. The package is then sealed and returned to ARISE to be added to the database. There is zero tolerance for error. If the sample arrives with an inaccurate identifier, it cannot be used and is a wasted opportunity to log a species.

ARISE needed a barcode reader that would be highly accurate and could deal with tiny Data Matrix codes in challenging outdoor conditions. It also needed to work offline, since many collectors are working in remote locations such as the North Sea, sand dunes or forests.

We needed to scan tiny Data Matrix codes through plastic bags, test tubes and liquid. Dynamsoft Barcode Reader had the high accuracy and offline capability that we needed."

– Lotte van Leengoed, Product Owner, Naturalis Biodiversity Center

Solution

The ARISE team had started out with an open source barcode reader, but quickly ran up against limitations. The scanner was unable to consistently read the tiny Data Matrix codes accurately and was unable to work offline. Also, since many mobile phones now have multiple camera lenses, they needed to be able to specify which camera lens was used to focus on the barcode. The scanning SDK also needed to work on both desktop and mobile.

With Dynamsoft Barcode Reader, the ARISE developers were able to see success quickly where the previous barcode reader had failed. Dynamsoft’s barcode scanner was able to read with close to 100% accuracy, even when scanning a tiny slip of paper floating in alcohol in a test tube inside a plastic bag.

Impact

The ARISE collection app will be rolled out to scientific expert collectors across the Netherlands. Collecting and logging specimens has not only become faster and easier, but now fewer specimens will be wasted due to ID code scanning errors. This is vitally important, since some species are in very remote areas, tricky to collect and are rarely seen.

Mapping the biodiversity of the Netherlands is far from a purely academic exercise. What it means is that scientists will be able to monitor the effects of environmental conditions on soil, air and water diversity much more quickly and easily. The ARISE consortium is also building a semi-automatic infrastructure to identify species using image and sound recognition and radar data.

Ultimately, they will able to take a water sample from a canal, run it through the system and see exactly which species are present and how it changes over time due to environmental influences. Previously, this would have meant a very lengthy, error prone process of manual sampling, picking out each individual species, identifying and logging it. When completed, the ARISE project will allow rapid, efficient environmental DNA monitoring and enable faster responses to changes in biodiversity.