3D scanning Lichens around Trinidad, California

During lockdown, I picked up the hobby of photogrammetry, also known as structure from motion (SfM) as a way to make models of my house plants. The fundamental concept of SfM is stitching together multiple angles of an object or a scene to create a computer estimate of the 3D object and a 2D texture that will be wrapped around it. This presents a powerful opportunity to be used as a dataset to capture 3D structure and spectral attributes of smaller organisms that would be challenging to measure without destroying them. There is numerous open-source software that can be used in tandem to create a powerful SfM workflow. The software that I used for this process are listed below, and documentation and tutorials can be found with a quick Google search.

Here are four locations where I took scans. This is by no means an exhaustive analysis of lichens in this area! Rather it is a little peek into a small detail of our world that is rarely appreciated.

Alder tree lichen mosaic

  • Location: Luffenholtz Beach (41.040331, -124.119902), 30 feet northwest of the parking lot along Scenic Drive.
  • Host species: Alnus rubra or another Alnus spp. , 15-20 feet tall
  • Lichen Species: Undetermined; potentially 3 different looking lichen species.
  • Behaviors: competition between different lichen species.
  • 3D Model Details: created from 86 images
  • Detail photo that was used in SfM model
  • 3D model
  • Overall view of 3D scan of Alder tree.

Conifer bark lichen

  • Location: Luffenholtz Beach (41.040331, -124.119902), 35 feet northwest of the parking lot along Scenic Drive.
  • Host species: Unidentified conifer tree
  • Lichen Species: Undetermined; 1 species of green lichen with prominent structures
  • Behaviors: There doesn’t appear to be competition because there are only one species
  • 3D Model Details: created from 86 images
  • Detail photo that was used in SfM model
  • 3D model detail
  • Overall view of 3D scan of conifer tree lichen.

Ocean Cliff lichen mosaic

  • Location: Luffenholtz Beach Cliffs (41.035593, -124.118539), at the end of the south trail
  • Substrate : Large cliff of dark-colored rock
  • Lichen Species: Undetermined; over 4 species of including some that are bright green, orange, white, and dark grey.
  • Behaviors: competition between different lichen species.
  • 3D Model Details: created from 79 images
  • Detail photo that was used in SfM model
  • 3D Model
  • Overall view of 3D scan of ocean facing cliff lichen.

Boulder lichen mosaic

  • Location: Moonstone Beach (41.029441, -124.111534), on west side of the parking lot.
  • Substrate : Dark-colored boulder
  • Lichen Species: Undetermined; at least 3 species
  • Behaviors: potential competition between lichen species as well as multiple with mosses and ferns.
  • 3D Model Details: created from 123 images
  • Complete 3D model
  • Zoom in of 3D Model
  • Reference Image
  • 3D model
Comparison between the reference image and the model render shows that the SfM method struggles to capture the branching nature of lichen. The reference image appears more bright and vibrant. The model does a good job of distinguishing between higher contrast surfaces.

What is Next?

In review, there are more things that I could do to improve the quality of the models in Meshroom. I could also put more work into cleaning up the model and retexturing and retopologizing it in Mesh Lab. The solution that will likely get me the best results next time is to focus on taking better quality photos so that the software will be able to create more feature matches, and therefore more detail. A greater number of pictures with higher amounts of overlap would also help create a higher resolution mesh.

Here are links to the software I used:

Here is a map of the Trinidad beaches that I visited. This is the land of the Wiyot people.