Fruit and seed of 'Ormosia emarginata' (left), fruit and seed of 'Sterculia lanceolata Cav.' Source: CUHK Shiu-Ying Hu Herbarium

Virtual herbarium to preserve HK ecology

30 November 2022

The online resource offers 3D seed models of more than 300 plants specimens, archived by the research team at Chinese University of Hong Kong’s Shiu-Ying Hu Herbarium.

Hong Kong now has its own mini version of the “Doomsday Vault”, referring to the Svalbard Global Seed Vault, located in the Arctic on a remote Norwegian archipelago. Since its official opening in 2008, the Svalbard genebank has preserved the seeds of almost every crop around the world to provide food security should apocalyptic events like climate crises, wars or natural disasters come to pass. At the Chinese University of Hong Kong’s Shiu-Ying Hu Herbarium, a team led by Dr David Lau Tai-wai has built a similar repository, albeit with less of an emphasis on doomsday scenarios. The innovative online database, the Virtual Carpological Herbarium of Fruits and Seeds, is intended not only for academic purposes, but also to educate the public about the importance of the local ecology.

From left, Dr David Lau Tai-wai, Wang Ho-lam, Wong Tin-hang, and Chan Yiu-man. Source: CUHK Shiu-Ying Hu Herbarium.

The idea for the database germinated back in 2017 when Lau travelled to South Korea. At one tourist attraction, he came across a photo booth equipped with a hundred cameras that took pictures from different angles to create 3D models of the travellers. He wondered: What if he were to apply similar technology to his botanical research on archiving local seeds and fruits?

Upon returning to Hong Kong, Lau and his team tried to find the most suitable equipment to get things started. “We need to show the fine features of the seeds in high resolution, and we are talking about some specimens with just two to three millimetres in diameter,” Lau said in an interview. Achieving that level of detail is not easy to do. However, the team managed to figure it out by using a DSLR camera and EF 100mm macro lens.

The settings of the photogrammetric platform. A DSLR camera was used to capture a total of 96 images of the specimen, fruit of 'Sterculia lanceolata Cav.', from three different vertical angles when the turntable rotated. Source: CUHK Shiu-Ying Hu Herbarium

Timing was critical, according to the first author of the research Wang Ho-lam, who was responsible for collecting samples from the field. “One of the challenges is we need to do the shooting on the same day or the next after collecting the seeds,” he said, “because the shape, colour and the size of the fresh seeds can be distorted very quickly. We need to race against time to archive what we got.”

Each specimen was labelled with a reference number and a voucher specimen number. Source: CUHK Shiu-Ying Hu Herbarium.

Another difficulty, according to Wong Tin-hang, the system engineer of Shiu-Ying Hu Herbarium, has been finding the right tools to digitise all the seeds gathered. The existing software and server each may have their own flaws. For example, the server might prompt advertisements that would distract or impede users as they interact with the 3D seed models; another consideration for the team has been the number of images required for constructing a single seed model. If they use too many images, this may overload the server with even a small amount of models. Eventually, the team set the requirements at 90 to 100 photographs per specimen to build the 3D model using the “structure-from-motion” technique.

In two years, the team successfully reconstructed more than 300 plant specimens into 3D models, of which 200 are native species. Lau underscored the importance of this research. “There are more than 200 native plant species in Hong Kong that are listed in IUCN Red List of Threatened Species, and more than one-sixth plant species found in Hong Kong are listed in Pharmacopoeia of the People’s Republic of China. It should be a priority to record these plants,” he explained.

The 3D plant model database is now available online for all to view on computers and mobile devices without additional software. Users can observe the models in fine detail by zooming in and out, rotating them as if viewing the objects as real physical specimens in an herbarium.

3D model of the fruit of Sterculia Lanceolata Cavanilles published on the Virtual Carpological Herbarium of Fruits and Seeds.

The work created by the team represents an extremely valuable resource to academic researchers as the 3D models facilitate identification of plant varieties and endangered species. By comparing the 3D models of carpological parts from multiple individuals of the same species with their genetic differences, researchers may have better visualisation and understanding on gene and phenotypic structure.

The team also hopes that the research may spark the interest of students prompting them to discover more about the local ecology. “Our research result has now been made into e-learning materials for School of Chinese Medicine CUHK,” Lau said. “We also keep in touch with Agriculture, Fisheries and Conservation Department (AFCD) to do incense tree plantation in local primary and secondary school campuses along with STEAM education programs. All we want is to raise awareness of protecting the valuable natural habitat of Hong Kong.”

In the short term, the team will maintain and improve the interface of the interactive online database, adding search filters for easier comparison of different seeds. “We need to collect more specimens,” Wang added. In ten years, the team plans to document nearly all the local plant species including the rare and endangered ones with AFCD. Such a database could be used to investigate and provide evidence of Hong Kong’s great biodiversity. “We hope to set an example for other botanists and herbaria to establish their own 3D databases, to allow knowledge transfer for generations,” Lau noted.

The methodology and results of making the database has recently been published in PLOS One, and you can explore the 3D models here