Journal Article
. 2021 May; 9:e11155.
doi: 10.7717/peerj.11155.

scAnt-an open-source platform for the creation of 3D models of arthropods (and other small objects)

Fabian Plum 1 David Labonte 1 
Affiliations
  • PMID: 33954036
  •     29 References

Abstract

We present scAnt, an open-source platform for the creation of digital 3D models of arthropods and small objects. scAnt consists of a scanner and a Graphical User Interface, and enables the automated generation of Extended Depth Of Field images from multiple perspectives. These images are then masked with a novel automatic routine which combines random forest-based edge-detection, adaptive thresholding and connected component labelling. The masked images can then be processed further with a photogrammetry software package of choice, including open-source options such as Meshroom, to create high-quality, textured 3D models. We demonstrate how these 3D models can be rigged to enable realistic digital specimen posing, and introduce a novel simple yet effective method to include semi-realistic representations of approximately planar and transparent structures such as wings. As a result of the exclusive reliance on generic hardware components, rapid prototyping and open-source software, scAnt costs only a fraction of available comparable systems. The resulting accessibility of scAnt will (i) drive the development of novel and powerful methods for machine learning-driven behavioural studies, leveraging synthetic data; (ii) increase accuracy in comparative morphometric studies as well as extend the available parameter space with area and volume measurements; (iii) inspire novel forms of outreach; and (iv) aid in the digitisation efforts currently underway in several major natural history collections.

Keywords: 3D; Digitisation; Macro imaging; Morphometry; Photogrammetry; Zoology.

Large-scale 3D imaging of insects with natural color.
Jia Qian, Shipei Dang, +10 authors, Ming Lei.
Opt Express, 2019 Mar 17; 27(4). PMID: 30876094
Nomenclatural benchmarking: the roles of digital typification and telemicroscopy.
Quentin Wheeler, Thierry Bourgoin, +6 authors, M Alma Solis.
Zookeys, 2012 Aug 04; (209). PMID: 22859888    Free PMC article.
To 3D or not to 3D, that is the question: do 3D surface analyses improve the ecomorphological power of the distal femur in placental mammals?
Francois D H Gould.
PLoS One, 2014 Mar 19; 9(3). PMID: 24633081    Free PMC article.
Assessment of North American arthropod collections: prospects and challenges for addressing biodiversity research.
Neil S Cobb, Lawrence F Gall, +3 authors, Akito Y Kawahara.
PeerJ, 2019 Dec 04; 7. PMID: 31788358    Free PMC article.
How long is the coast of britain? Statistical self-similarity and fractional dimension.
B Mandelbrot.
Science, 1967 May 05; 156(3775). PMID: 17837158
Highly Cited.
No specimen left behind: industrial scale digitization of natural history collections.
Vladimir Blagoderov, Ian J Kitching, +2 authors, Vincent S Smith.
Zookeys, 2012 Aug 04; (209). PMID: 22859884    Free PMC article.
scikit-image: image processing in Python.
Stéfan van der Walt, Johannes L Schönberger, +6 authors, scikit-image contributors.
PeerJ, 2014 Jul 16; 2. PMID: 25024921    Free PMC article.
Highly Cited.
Fast animal pose estimation using deep neural networks.
Talmo D Pereira, Diego E Aldarondo, +4 authors, Joshua W Shaevitz.
Nat Methods, 2018 Dec 24; 16(1). PMID: 30573820    Free PMC article.
Highly Cited.
Phylogenomics resolves the timing and pattern of insect evolution.
Bernhard Misof, Shanlin Liu, +98 authors, Xin Zhou.
Science, 2014 Nov 08; 346(6210). PMID: 25378627
Highly Cited.
Static/Dynamic Filtering for Mesh Geometry.
Juyong Zhang, Bailin Deng, +3 authors, Ligang Liu.
IEEE Trans Vis Comput Graph, 2018 Jul 12; 25(4). PMID: 29993982
An automated device for the digitization and 3D modelling of insects, combining extended-depth-of-field and all-side multi-view imaging.
Bernhard Ströbel, Sebastian Schmelzle, Nico Blüthgen, Michael Heethoff.
Zookeys, 2018 Jun 02; (759). PMID: 29853774    Free PMC article.
DeepLabCut: markerless pose estimation of user-defined body parts with deep learning.
Alexander Mathis, Pranav Mamidanna, +4 authors, Matthias Bethge.
Nat Neurosci, 2018 Aug 22; 21(9). PMID: 30127430
Highly Cited.
A Practical Guide to Sliding and Surface Semilandmarks in Morphometric Analyses.
C Bardua, R N Felice, +2 authors, A Goswami.
Integr Org Biol, 2019 Jul 05; 1(1). PMID: 33791531    Free PMC article.
Measurement error in geometric morphometrics.
Carmelo Fruciano.
Dev Genes Evol, 2016 Apr 03; 226(3). PMID: 27038025
Review.
Computational Analysis of Behavior.
S E Roian Egnor, Kristin Branson.
Annu Rev Neurosci, 2016 Apr 20; 39. PMID: 27090952
Review.
DeepPoseKit, a software toolkit for fast and robust animal pose estimation using deep learning.
Jacob M Graving, Daniel Chae, +4 authors, Iain D Couzin.
Elife, 2019 Oct 02; 8. PMID: 31570119    Free PMC article.
R(2)OBBIE-3D, a Fast Robotic High-Resolution System for Quantitative Phenotyping of Surface Geometry and Colour-Texture.
António F Martins, Michel Bessant, Liana Manukyan, Michel C Milinkovitch.
PLoS One, 2015 Jun 04; 10(6). PMID: 26039509    Free PMC article.
Inselect: Automating the Digitization of Natural History Collections.
Lawrence N Hudson, Vladimir Blagoderov, +5 authors, Vincent S Smith.
PLoS One, 2015 Nov 26; 10(11). PMID: 26599208    Free PMC article.
Distinguishing seemingly indistinguishable animals with computer vision.
Kristin Branson.
Nat Methods, 2014 Jun 28; 11(7). PMID: 24972171
Mass digitization of scientific collections: New opportunities to transform the use of biological specimens and underwrite biodiversity science.
Reed S Beaman, Nico Cellinese.
Zookeys, 2012 Aug 04; (209). PMID: 22859875    Free PMC article.
2D or Not 2D? Testing the Utility of 2D Vs. 3D Landmark Data in Geometric Morphometrics of the Sculpin Subfamily Oligocottinae (Pisces; Cottoidea).
Thaddaeus J Buser, Brian L Sidlauskas, Adam P Summers.
Anat Rec (Hoboken), 2017 Dec 16; 301(5). PMID: 29244247
Exploiting Visibility Information in Surface Reconstruction to Preserve Weakly Supported Surfaces.
Michal Jancosek, Tomas Pajdla.
Int Sch Res Notices, 2014 Jan 01; 2014. PMID: 27437454    Free PMC article.
Machine vision methods for analyzing social interactions.
Alice A Robie, Kelly M Seagraves, S E Roian Egnor, Kristin Branson.
J Exp Biol, 2017 Jan 07; 220(Pt 1). PMID: 28057825
Review.
Capturing natural-colour 3D models of insects for species discovery and diagnostics.
Chuong V Nguyen, David R Lovell, Matt Adcock, John La Salle.
PLoS One, 2014 Apr 25; 9(4). PMID: 24759838    Free PMC article.
Automated image-based tracking and its application in ecology.
Anthony I Dell, John A Bender, +8 authors, Ulrich Brose.
Trends Ecol Evol, 2014 Jun 09; 29(7). PMID: 24908439
Highly Cited. Review.
Testing accuracy in 2D and 3D geometric morphometric methods for cut mark identification and classification.
Lloyd A Courtenay, Miguel Ángel Maté-González, +3 authors, Manuel Domínguez-Rodrigo.
PeerJ, 2018 Jul 14; 6. PMID: 30002969    Free PMC article.
An experimental comparison of min-cut/max-flow algorithms for energy minimization in vision.
Yuri Boykov, Vladimir Kolmogorov.
IEEE Trans Pattern Anal Mach Intell, 2005 Mar 04; 26(9). PMID: 15742889
Highly Cited.
Whole-drawer imaging for digital management and curation of a large entomological collection.
Beth Louise Mantle, John La Salle, Nicole Fisher.
Zookeys, 2012 Aug 04; (209). PMID: 22859885    Free PMC article.
anTraX, a software package for high-throughput video tracking of color-tagged insects.
Asaf Gal, Jonathan Saragosti, Daniel Jc Kronauer.
Elife, 2020 Nov 20; 9. PMID: 33211008    Free PMC article.