3D modelling

Having fun while doing research… or doing research while having fun?!?!?

The new frontiers of technology are starting paying dividends for me as well, finally. I’m talking about 3D modelling. A couple of months ago I finalize my morphological analysis on Cystophora species (I’ll be talking about them in another article) mainly aimed to test the hypothesis that a different morphology can be a good driver for clients (abundance, biodiversity, ecc). Scientific literature has already reported how biogenic architecture can be extremely relevant for invertebrates in intertidal and subtidal marine communities and many ways have been found to study, quantifying and comparing the tridimensionality of key-stone or common species.


My research in this field started with high-quality pictures and since I’m very keen in graphics… well, I ended up with looking for informations about 3d modelling.

During my studies in experimental ecology, I’ve used (and I’m currently using) lot of different materials with different shape and size in order to emulate habitat-formers and epiphytes, for morphological reasons and ecological processes.
Here is when 3D modelling can help research in testing how several variables are affected by some specific factors.

That’s a good chance to mention a free software (with additional feature through payment): Autodesk Memento, with the new version Autodesk Remake, is an excellent software able to manage with a series of pictures or scans from laser or 3D scanners and output a tridimensional model.

Obviously I’ve already tried it (how to resist?!?!) with a Canon Powershot G15, collecting a series of sequential 360 degrees pictures at different height with the right light and background. Creating a 3D model can be really easier than the expected if you do it in the right way.

Here are a couple of models I’ve created some months ago. The mussel was kind of 15 cm while the cockle was more and less 2-2.5 cm long.
They are definitely incredibly accurate (note all the epibionts living in the mussel) and the resolution is excellent (thanks the camera) allowing in some case really complex analysis.
Their use is mainly addressed to test the role of this organisms in their habitat, defining the consequences of replacing them with mimics or modifying some factors strictly related with their ecology or morphology (temperature, color, rugosity, etc).




What next? Well, I’ll post something… :)


FCs are pretty widespread phenomena but they have attracted interest only in the last 15-20 years. Then, my research begin where the few information about them stop.

In order to have a broad understanding of the role of HC in ecology, I am currently working in different marine environments (soft-bottom estuarines and rocky shores), with different 1st habitat formers (seaweeds, seageasses, invertebrates) and different 2nd habitat formers and clients (epiphytes, invertebrates).

a and b reppresent two typical situations in soft-bottom estuarines. Due to lack of hard substrates, seaweeds can only rely in molluscs to settle (a) or seagrasses to be entagled (b) becoming 2nd habitat former. In rocky shores, a similar situation can be explained through epiphytes (c) but lack of substrate is not a problem anymore unless considering the competition.

What among seaweeds?

Even if Facilitation Cascade seems to be simple concept to understand it is in real much more complicate than the expected… and even if it looks very complex, it is in real much easier than the expected…

After a quick explanation about my research, especially when I talk about hundreds or thousands of invertebrates among seaweeds, people usually look at me with that typical face like wondering “What is he talking about? Where does he see all these organisms?“.

Unfortunately, our mind (scientific and not) has always been pretty restricted to allow us to give importance to what is invisible, small… (I remind the “conquest of the invisible” by Pasteur) neglecting a huge amount of species, interactions, functions, biological processes, etc… in a single word… “information“.

It seems to be hard accepting the idea that a little piece of seaweed can host a huge amount of species. That is why in this short clip I try to visually demonstrate what happen when we wash a little piece of seaweed collected from a rocky shore.
The seaweed is a Cystophora scalaris, one of the species I am working most with, and it is a very common canopy-forming seaweed in the rocky shores of New Zealand (Agardh used to relate it to Cystopseira sp. and Sargassum sp. from Mediterranean Sea because of their common role as facilitators in coastal habitats).

The majority of little dots at the bottom of the box are gastropods… but there are still hundreds of invertebrates pretty invisible to the naked eye in a box like this, like amphipods and copepods. The pictures show a clearer view of the epifauna more accurately sieved.


In the following clip I show what happen when we compare the amount of invertebrates in two pieces of the same seaweed species. The first one is a piece of C. scalaris while the second one is a piece of C. scalaris with attached, during a recolonization experiment, a little piece of a natural epiphyte of Cystophora, Jania micrarthrodia.

The difference in the amount of invertebrates is pretty clear. Even if I manually attached the epiphyte, Jania is a natural epiphyte of Cystophora, so what is experimentally happening here is just the emulation of a natural condition. But there is something more…
After deattaching Jania from Cystophora, I can rinse the epiphyte more accurately…

Obviously this quick clip does not want to have any scientific relevance and it is mean to give a very rough idea of what happen when an epiphyte increases the complexity of a seaweed structure and architecture with full advantage for the associated epifaunal assemblage.
Several are the factors here not included: the different size of the seaweed, the rest of smaller and “invisible” invertebrates for naked eye, the accuracy of the washing, etc.
Anyway, a more true view of the invertebrates can be offered by the next pictures, after an accurate sieving.

The epifauna I am considering has usually a size range between 250 μm and 2 mm and the majority of these are amphipods, copepods and gastropods.
In my PhD I am focus on the whole community of invertebrates. Nonetheless my primary focus are gastropods since they can be considered very reppresentative of the epifauna community for my purposes:
– they are slow-moving invertebrates compared with amphipods, copepods or crabs, so they can be collected easly without any virtual lack of information;
– they are relatively easy to identify, at least with a categorization based on morpho-species;
– they reppresent a very high proportion of the community, statistically strong, and a very diverse category of invertebrates: in my studies, gastropods reppresent more and less the 60-70% of the whole biodiversity.