Review

. 2022 Aug 4;25(9):104867.

doi: 10.1016/j.isci.2022.104867. eCollection 2022 Sep 16.

3D visualization processes for recreating and studying organismal form

Duncan J Irschick¹, Fredrik Christiansen², Neil Hammerschlag^{3

4

5}, Johnson Martin⁶, Peter T Madsen^{7

2}, Jeanette Wyneken⁸, Annabelle Brooks⁹, Adrian Gleiss^{10

11}, Sabrina Fossette¹², Cameron Siler¹³, Tony Gamble^{14

15

16}, Frank Fish¹⁷, Ursula Siebert¹⁸, Jaymin Patel¹⁹, Zhan Xu²⁰, Evangelos Kalogerakis²⁰, Joshua Medina¹, Atreyi Mukherji²¹, Mark Mandica²², Savvas Zotos^{23

24}, Jared Detwiler²⁵, Blair Perot²⁶, George Lauder²⁷

Affiliations

¹ Department of Biology, 221 Morrill Science Center, University of Massachusetts, Amherst, MA 01003, USA.
² Aarhus Institute of Advanced Studies, Høegh-Guldbergs Gade 6B, Aarhus C, Denmark.
³ Rosenstiel School of Marine and Atmospheric Science, University of Miami, Miami, FL, USA.
⁴ Leonard and Jayne Abess Center for Ecosystem Science and Policy, University of Miami, Coral Gables, FL, USA.
⁵ Shark Research and Conservation Program, University of Miami, Miami, FL, USA.
⁶ 329 E Main Street, Wilmore, KY 40390, USA.
⁷ Zoophysiology, Department of Biology, Aarhus University, Aarhus, Denmark.
⁸ Department of Biological Sciences, Florida Atlantic University, 777 Glades Road, Boca Raton, FL 33431-0991, USA.
⁹ Cape Eleuthera Institute, PO Box EL-26029, Rock Sound, Eleuthera, The Bahamas.
¹⁰ Centre for Sustainable Aquatic Ecosystems, Harry Butler Institute, Murdoch University, 90 South Street, Murdoch, WA 6150, Australia.
¹¹ College of Science, Health, Engineering and Education, Murdoch University, 90 South St, Murdoch, WA 6150, Australia.
¹² Biodiversity and Conservation Science, Department of Biodiversity, Conservation and Attractions, 17 Dick Perry Avenue, Kensington, WA 6151, Australia.
¹³ Sam Noble Oklahoma Museum of Natural History and Department of Biology, University of Oklahoma, 2401 Chautauqua Avenue, Norman, OK 73072-7029, USA.
¹⁴ Marquette University, Wehr Life Sciences 109, 1428 W. Clybourn Street, Milwaukee, WI 53233, USA.
¹⁵ Milwaukee Public Museum, 800 W. Wells Street, Milwaukee, WI 53233, USA.
¹⁶ Bell Museum of Natural History, University of Minnesota, 1987 Upper Buford Circle, St. Paul, Minnesota 551088, USA.
¹⁷ Department of Biology, West Chester University, West Chester, PA 19383, USA.
¹⁸ Institute for Terrestrial and Aquatic Wildlife Research, University of Veterinary Medicine, Hannover, Werftstrasse 6, 25761 Buesum, Germany.
¹⁹ Temple University Kornberg School of Dentistry, 3223 North Broad Street Philadelphia, PE 19140, USA.
²⁰ College of Information and Computer Sciences, University of Massachusetts, 140 Governors Dr., Amherst, MA, USA.
²¹ University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA.
²² Amphibian Foundation, 4055 Roswell Road NE, Atlanta, GA 30342, USA.
²³ Terra Cypria-the Cyprus Conservation Foundation, Agiou Andreou 341, 3035 Limassol, Cyprus.
²⁴ School of Pure and Applied Sciences, Open University of Cyprus, PO Box 12794, 2252 Nicosia, Cyprus.
²⁵ 22 Hooker Avenue Unit 1, Northampton, MA 01060, USA.
²⁶ Department of Mechanical and Industrial Engineering, University of Massachusetts, Amherst, MA 01003-2210, USA.
²⁷ Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138, USA.

PMID: 36060053
PMCID: PMC9437858
DOI: 10.1016/j.isci.2022.104867

Review

3D visualization processes for recreating and studying organismal form

Duncan J Irschick et al. iScience. 2022.

. 2022 Aug 4;25(9):104867.

doi: 10.1016/j.isci.2022.104867. eCollection 2022 Sep 16.

Authors

Affiliations

¹ Department of Biology, 221 Morrill Science Center, University of Massachusetts, Amherst, MA 01003, USA.
² Aarhus Institute of Advanced Studies, Høegh-Guldbergs Gade 6B, Aarhus C, Denmark.
³ Rosenstiel School of Marine and Atmospheric Science, University of Miami, Miami, FL, USA.
⁴ Leonard and Jayne Abess Center for Ecosystem Science and Policy, University of Miami, Coral Gables, FL, USA.
⁵ Shark Research and Conservation Program, University of Miami, Miami, FL, USA.
⁶ 329 E Main Street, Wilmore, KY 40390, USA.
⁷ Zoophysiology, Department of Biology, Aarhus University, Aarhus, Denmark.
⁸ Department of Biological Sciences, Florida Atlantic University, 777 Glades Road, Boca Raton, FL 33431-0991, USA.
⁹ Cape Eleuthera Institute, PO Box EL-26029, Rock Sound, Eleuthera, The Bahamas.
¹⁰ Centre for Sustainable Aquatic Ecosystems, Harry Butler Institute, Murdoch University, 90 South Street, Murdoch, WA 6150, Australia.
¹¹ College of Science, Health, Engineering and Education, Murdoch University, 90 South St, Murdoch, WA 6150, Australia.
¹² Biodiversity and Conservation Science, Department of Biodiversity, Conservation and Attractions, 17 Dick Perry Avenue, Kensington, WA 6151, Australia.
¹³ Sam Noble Oklahoma Museum of Natural History and Department of Biology, University of Oklahoma, 2401 Chautauqua Avenue, Norman, OK 73072-7029, USA.
¹⁴ Marquette University, Wehr Life Sciences 109, 1428 W. Clybourn Street, Milwaukee, WI 53233, USA.
¹⁵ Milwaukee Public Museum, 800 W. Wells Street, Milwaukee, WI 53233, USA.
¹⁶ Bell Museum of Natural History, University of Minnesota, 1987 Upper Buford Circle, St. Paul, Minnesota 551088, USA.
¹⁷ Department of Biology, West Chester University, West Chester, PA 19383, USA.
¹⁸ Institute for Terrestrial and Aquatic Wildlife Research, University of Veterinary Medicine, Hannover, Werftstrasse 6, 25761 Buesum, Germany.
¹⁹ Temple University Kornberg School of Dentistry, 3223 North Broad Street Philadelphia, PE 19140, USA.
²⁰ College of Information and Computer Sciences, University of Massachusetts, 140 Governors Dr., Amherst, MA, USA.
²¹ University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA.
²² Amphibian Foundation, 4055 Roswell Road NE, Atlanta, GA 30342, USA.
²³ Terra Cypria-the Cyprus Conservation Foundation, Agiou Andreou 341, 3035 Limassol, Cyprus.
²⁴ School of Pure and Applied Sciences, Open University of Cyprus, PO Box 12794, 2252 Nicosia, Cyprus.
²⁵ 22 Hooker Avenue Unit 1, Northampton, MA 01060, USA.
²⁶ Department of Mechanical and Industrial Engineering, University of Massachusetts, Amherst, MA 01003-2210, USA.
²⁷ Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138, USA.

PMID: 36060053
PMCID: PMC9437858
DOI: 10.1016/j.isci.2022.104867

Abstract

The study of biological form is a vital goal of evolutionary biology and functional morphology. We review an emerging set of methods that allow scientists to create and study accurate 3D models of living organisms and animate those models for biomechanical and fluid dynamic analyses. The methods for creating such models include 3D photogrammetry, laser and CT scanning, and 3D software. New multi-camera devices can be used to create accurate 3D models of living animals in the wild and captivity. New websites and virtual reality/augmented reality devices now enable the visualization and sharing of these data. We provide examples of these approaches for animals ranging from large whales to lizards and show applications for several areas: Natural history collections; body condition/scaling, bioinspired robotics, computational fluids dynamics (CFD), machine learning, and education. We provide two datasets to demonstrate the efficacy of CFD and machine learning approaches and conclude with a prospectus.

Keywords: Biological sciences; Ecology; Evolutionary biology; Zoology.

PubMed Disclaimer

Conflict of interest statement

The authors declare no conflict of interest.

Figures

**Figure 1**
3D photogrammetry methods for reconstructing live animals Multi-camera scanning methods for photo-scanning various kinds of animals using 3D digital photogrammetry, such as small reptiles; (A) a tokay gecko, *Gekko gecko*, taken in the Irschick lab at the University of Massachusetts at Amherst, USA); (B) a medium sized sea turtle (a green sea turtle, *Chelonia mydas*, taken at the Loggerhead MarineLife Center, USA); (C) a large mammal (a southern white rhino (*Ceratotherium simum*, taken at the Perth zoo, Australia); A typical process for 3D photogrammetry of live specimens, including multiple photos (D), creation of a 3D surface using 3D software (E), and finally a full-color version (F) which closely replicates the original specimen. Photos are of a marine toad (*Rhinella marina*) taken in the Philippines.

**Figure 2**
3D shapes of various animal species 3D whole body meshes of the 14 described species in Table 1, which are: (A) southern right whale (*Eubalaena australis*), (B) southern white rhino (*Ceratotherium simum simum*), (C) blacktip shark (*Carcharhinus limbatus*), (D) harbor porpoise (*Phocoena phocoena*), (E) loggerhead sea turtle, *Caretta caretta*, (F) flatback sea turtle (*Natator depressus*), (G) green sea turtle (*Chelonia mydas*), (H) kemps Ridley sea turtle (*Lepidochelys kempii,* (I), hawksbill sea turtle (*Eretmochelys imbricata*), (J) Cyprus racer snake (*Dolichophis jugularis*), (K) sling-tailed agama (*Stellagama stellio cypriaca*), (L) tokay gecko (*Gekko gecko*), (M) flying gecko (*Ptychozoon kuhli*), (N) house gecko (*Hemidactylus platyurus*).

**Figure 3**
Scaled volumetric 3D models of the 14 animal species in Table 1, showing the variation in body size, volume and surface area Animals are shown from the largest to smallest. The southern right whale is not shown, as it is too large.

**Figure 4**
Scaling parameters from 3D models A plot of estimated mass versus surface area (A), and mass versus volume (B) for 12 of the 14 animal species in Table 1 (no mass data were available for the flatback sea turtle or the blacktip shark).

**Figure 5**
Swimming parameters for scaled green sea turtle 3D model Plots of swimming speed (x axis) versus swimming thrust force (A), swimming power (B), and standardized swimming power (C) based on computational fluids dynamics (CFD) simulations for three simulated age classes from 3D models of green sea turtles (*Chelonia mydas*).

**Figure 6**
Input and output of the machine learning method outlined in Data S3 Given an input video capturing the motion of a live chain catshark (*Scyliorhinus retifer*). (A) Our method automatically generates animations of several fish-like models closely following the captured motion. (B) We also refer to our Video S1 showing the whole motion.

**Figure 7**
Pipeline of the machine learning method outlined in Data S3 (A–D) given an input 3D model, created through photogrammetry or modeled by an artist, (B) our method employs a neural network to rig it with an animation skeleton, then (C) using an input video capturing the locomotion of a real animal, (D) another neural network controls the skeleton and animates the 3D model so that its motion closely follows the input video.

See this image and copyright information in PMC

References

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3D visualization processes for recreating and studying organismal form

Affiliations

3D visualization processes for recreating and studying organismal form

Authors

Affiliations

Abstract

Conflict of interest statement

Figures

References

Publication types

LinkOut - more resources

Full Text Sources

Miscellaneous