Imagine a fern, tucked away in a botanical garden, that unfurls. By next week it’ll look different and by next season it may even be gone. Plants are living organisms that are constantly changing and can be fragile which makes them hard to document.
For instance, a pressed specimen in a herbarium captures a plant in two dimensions and at a single moment. While a photograph shows one angle at a time, leaving a lot of this detail hidden.
Researchers at the University of Tartu in Estonia have recently published a study in Biodiversity Data Journal showing a practical alternative: using ordinary cameras to build detailed, explorable 3D models of plants, from a single orchid flower to an entire tropical greenhouse.
Why 3D matters for plants
Branching patterns, the spiral arrangement of leaves, the curl of a petal and the structure of a flower are all traits biologists use to identify species and understand growth, yet they are hard to judge from a flat image. A 3D model preserves them.
You can rotate it, zoom in and view it from angles the photographer never chose. For gardens and museums, that means a plant can be documented, shared and studied by someone on the other side of the world.
What the researchers did
The team combined two techniques. The first, photogrammetry, works out the 3D shape of an object from many overlapping photographs. It produces solid, measurable models, which makes it good for scientific measurement.
The second, 3D Gaussian Splatting, is a newer technique that represents a scene as millions of tiny, soft-edged blobs of colour. It renders in real time and looks strikingly photorealistic, especially for wispy, tangled vegetation that traditional methods struggle with.
Using modest equipment, mostly a compact Olympus TG-6 camera supplemented by a macro-lens camera, a smartphone and a drone, they applied both techniques to a range of subjects.
The researchers photographed a fern outdoors in a botanical garden on twelve days across a fifteen-day period, with roughly 8,500 photos in total. They captured the garden’s tropical greenhouse in fourteen overlapping sections, using about 20,000 photos, and stitched these into an interactive virtual walkthrough.
They also modelled a potted plant, an orchid photographed with an entry-level smartphone, close-up macro shots of flowers, and a tree filmed from a drone. Enjoy the orchid model below:
Watching a plant grow in 4D
The most striking result is the fern series, which the authors call “4D” because it adds time to the three spatial dimensions. Instead of fixing cameras in place, as many growth-monitoring systems do, the researchers aligned all photos from all days in a single project, using stable background features as reference points.
Each day’s model then shared the same scale and orientation, so growth could be compared directly. The result is a time-lapse you can walk around, allowing growth to be tracked without touching the plant or installing expensive equipment.
After running thousands of photogrammetric scans I realised that not all the images have to be directly related. While two pieces of fern won’t share many comparable feature points, the surrounding area has lots of them — for free!
– said the lead author, Toivo Ylinampa of University of Tartu.
Having a digital twin?
Living collections are irreplaceable, yet vulnerable to disease, climate stress, renovation and age. A digital twin cannot replace a living plant, but it can record what existed, where it grew and how it looked at a given moment.
Rare species can be documented far more richly than a single photo allows, and people who cannot travel can still explore a garden. Repeating the capture over time can also reveal how plants respond to their environment, and because the method relies on consumer cameras and widely available software, even small institutions can afford to try it.
The limitations
The effect of wind in 3D reconstruction. Windy conditions on the left resulted in inferior 3D reconstruction. Credit to Toivo Ylinampa and Urmas Kõljalg, 2026.
Despite the tremendous potential of this methodology, the researchers encountered several limitations. Wind was the biggest problem, with even gentle leaf movement noticeably degrading model quality, so calm days were essential.
Also, the greenhouse sections were stitched together by hand, so the walkthrough was suited to visual exploration rather than precise measurement, and processing was demanding, with the fern alignment taking about seven hours and 48 GB of memory. The two techniques play different roles: photogrammetry is better for measurement (a macro flower measured 13 mm on the model against 13.2 mm with calipers), while Gaussian Splatting better captures delicate structures such as hanging flowers.
As these tools become easier to use, every botanical garden could one day have a digital twin helping to document and preserve its species.
Original source and more 3D models:
Ylinampa T, Kõljalg U (2026) Photogrammetry and 3D Gaussian Splatting for 4D plant growth capture and greenhouse digital twins. Biodiversity Data Journal 14: e191083. https://doi.org/10.3897/BDJ.14.e191083
