Capturing Natural-Colour 3D Models of Insects for Species Discovery and Diagnostics

Abstract

Collections of biological specimens are fundamental to scientific understanding and characterization of natural diversity—past, present and future. This paper presents a system for liberating useful information from physical collections by bringing specimens into the digital domain so they can be more readily shared, analyzed, annotated and compared. It focuses on insects and is strongly motivated by the desire to accelerate and augment current practices in insect taxonomy which predominantly use text, 2D diagrams and images to describe and characterize species. While these traditional kinds of descriptions are informative and useful, they cannot cover insect specimens “from all angles” and precious specimens are still exchanged between researchers and collections for this reason. Furthermore, insects can be complex in structure and pose many challenges to computer vision systems. We present a new prototype for a practical, cost-effective system of off-the-shelf components to acquire natural-colour 3D models of insects from around 3 mm to 30 mm in length. (“Natural-colour” is used to contrast with “false-colour”, i.e., colour generated from, or applied to, gray-scale data post-acquisition.) Colour images are captured from different angles and focal depths using a digital single lens reflex (DSLR) camera rig and two-axis turntable. These 2D images are processed into 3D reconstructions using software based on a visual hull algorithm. The resulting models are compact (around 10 megabytes), afford excellent optical resolution, and can be readily embedded into documents and web pages, as well as viewed on mobile devices. The system is portable, safe, relatively affordable, and complements the sort of volumetric data that can be acquired by computed tomography. This system provides a new way to augment the description and documentation of insect species holotypes, reducing the need to handle or ship specimens. It opens up new opportunities to collect data for research, education, art, entertainment, biodiversity assessment and biosecurity control.

Use of Image Based Modelling for Documentation of Intricately Shaped Objects

“…In case of 3D models, the details rendered and overall quality of the model strongly determine possibilities and depth of study scientists are subsequently able to attain. As discussed in (Nguyen, 2014), there are several technical challenges to be addressed when attempting to scan relatively fragile objects of a several mm to few cm size. Approached by Slovak Academy of Sciences experts, we were tasked to give it a try with special intent of capturing fine details (legs, antennae) of the specimen.…”

“…A rather complex problems in areas of photographic optics, depth of field and coverage the object's surface geometry had to be addressed. The basic setup used in (Nguyen, 2014) was partially applied and modified in order to achieve improved high fidelity results. …”

Towards web-based semantic enrichment of 3D insects

“…Previously, we have outlined a system capable of digitizing small insect specimens into a highly detailed color mesh [Nguyen et al 2014]. This automated, photo-based system captures gigabytes of image data and produces a fully 3D mesh of around 10-20MB that is comparable in quality to the original photographs.…”

Natural-color 3D insect models for education, entertainment, biosecurity and science

“…The three main steps of the creating a natural-color 3D model of specimen are (1) mounting the insect onto a pin, (2) capture of high-magnification and depth-extended 2D images of the specimen at different poses, and (3) reconstruction of a single 3D model from those multiple images [Nguyen et al 2014a]. Our hardware setup can be seen in Figure 1.…”