Cal Poly Humboldt, Home of the World’s First 3D Herbarium

By Griffin Mancuso and Savana Robinson

Last Thursday, on the third floor of Cal Poly Humboldt’s library, a very important first birthday was celebrated. Students, faculty and community members gathered to enjoy cake, pizza, pie and refreshments to celebrate the launch of the world’s first 3D herbarium. 

Hosted at 3dherbarium.org, the 3D herbarium has digitized 3D models of various plants with information on each species. At time of publication, 39 models are available to view. From the seaside daisy, Erigeron glaucus, to the coast redwood, Sequoia sempervirens, each plant’s page has a classification breakdown, profile and information on the model itself.

Library Dean Cyril Oberlander started the opening speech for the event, thanking everyone for attending and emphasizing the project’s testament to hard work, dedication and collaborative efforts.

“We chose 3D modeling of plants because, well, not really anybody was doing it,” Oberlander said. “You can imagine how hard it is to do a three-dimensional shape of a two-dimensional leaf. While creating the 3D digital herbarium has never been done — and because plants are so crucial to life on Earth, and for our understanding of plants — this was incredibly important.”

The project has been in development for over a year and students have been anticipating its release, including botany major Juniper Beke.

“Last semester, I believe it was teased at the end of a session on satellite information using satellite data,” Beke said. “[The teaser] had appeared there at the end and so I was hyped up for it.”

Many students, like engineering and community practices major Filip Amborski, had ideas for what the program could accomplish. Amborski thinks the herbarium will be a great resource.

“I’m hoping that they have notes on anything that’s been identified as culturally significant to Native tribes,” Amborski said.

The seeds of inspiration

The 3D herbarium was created by Team Flora, which is comprised of computer science and botany students. Botany graduate student Heather Davis, undergraduate botany student Grayson Prater and computer science major David Yaranon helped create the website under the management of computer science graduate AJ Bealum.

AJ Bealum, computer science graduate and manager of Team Flora, credited the idea for the 3D herbarium to Oberlander. The university library was the sole sponsor for this project.

“His main source of inspiration was the anatomage table downstairs and he thought, ‘Why isn’t anyone doing this with plants?’” Bealum said.

Located on the second floor of the library, the anatomage table is a 3D human anatomy system where users can simulate cadaver dissection.

Prater wanted to join Team Flora to bring botany to those unfamiliar with the topic and introduce them to scientific language. Through this project, he has learned about programming and the difficulties that come with scanning plants.

“I really love writing about plants. This was a great job to start doing that and practicing that skill, especially science communication, making botany accessible to other non-botanists,” Prater said.

Davis accepted the position on Team Flora to satiate her passion for bringing the joy of botany to others. Her decision to join the team was inspired by Oscar Vargas of the botany department. Vargas is an assistant professor at Cal Poly Humboldt and director of the university’s Vascular Plant Herbarium.

“Dr. Oscar Vargas has been my professor, mentor and boss for the last couple of years,” Davis said. “Over the summer last year, the job got posted and he had been talking to AJ, so he reached out to me and sent me the link for the herbarium. I applied for it after that and joined the team.”

Current growth

The 3D herbarium website currently has a collection of 3D plant models, plant photos contributed from around the world and a plant identification component. 

Each 3D model was created using a process called photogrammetry. Photogrammetry requires around 100 to 300 photos of a single plant from many different angles in order to convert it into a 3D model. Yaranon created many of the plant models for the 3D herbarium.

“As you take more photos, the processing time increases exponentially,” Yaranon said. “In the beginning, we were running these off of rented laptops from the library, so we would have to wait a couple of days per model. Now we’re on a server, so we can put these out a lot quicker.” 

Davis collaborated with the computer scientists on Team Flora to annotate each plant model. She collected plant specimens for Bealum and Yaranon to photograph and create a model from. Then, she annotated different parts of the plant model with information for people with all levels of experience.

“It’s a really challenging subject for many people when they’re first introduced to it, especially with the names and all of the different scientific terms you have to learn,” Davis said. “So this project has been [a] really fun [way] to be able to give access to that knowledge and to make it a fun, engaging activity, instead of challenging and being afraid of a new topic.”

The herbarium also adds to its database with photos from iNaturalist, a website that allows users to upload photos of plants and animals to create a public database. Visitors can search up the common or scientific name of a plant and peruse a gallery with hundreds of photos taken around the world.

Additionally, the website has a plant identification program. Once a photo of a plant is uploaded, the program will provide a list of possible species and a short description. The program pulls from websites like Wikipedia, iNaturalist and the Global Biodiversity Information Facility.

Plan(ts) for the future

During the opening speech, Oberlander announced a planned second version of the 3D herbarium. The day before the ceremony, Team Flora got approval to start a full grant proposal to the Institute for Museum Library Services to get funding for further development of the program. Version two will include models that are applicable for other majors like anthropology or zoology. Oberlander mentioned that Team Flora hopes to receive the funding this summer.

“Our next version is going to be something that is anything that wants to be a 3D model, whether it’s art or something else. People can do all sorts of things with this 3D exhibit tool,” Oberlander said. “It’s either intended for students with projects or a classroom that wants to use this as a lab notebook, as opposed to the print version.”

Team Flora also hopes for other groups on campus to contribute to the 3D herbarium. They plan to make the process of photogrammetry more accessible so that clubs or classes can add to the website’s model collection. Bealum described meeting with the mycology club to help them learn how to use photogrammetry software so they could produce a fungus model for the website.

“Our ultimate goal with this [website] is to make it a school-incorporated tool,” Bealum said. “So that instead of us sitting in our office trying to pump out these 3D models and working with the botany students as assistants, the botany department can ultimately kind of take this over. [They can] make it a part of their classes, make it so that students can submit models as part of a class.”