New Method for Rapid 3D Reconstruction of Semi-Transparent Underwater Animals and Structures

Overview

Journal Integr Org Biol

Publisher Oxford University Press

Specialty Biology

Date 2023 Jul 31

PMID 37521145

Authors

Joost Daniels

Giovanna Sainz

Kakani Katija

Affiliations

Soon will be listed here.

Abstract

Morphological features are the primary identifying properties of most animals and key to many comparative physiological studies, yet current techniques for preservation and documentation of soft-bodied marine animals are limited in terms of quality and accessibility. Digital records can complement physical specimens, with a wide array of applications ranging from species description to kinematics modeling, but options are lacking for creating models of soft-bodied semi-transparent underwater animals. We developed a lab-based technique that can live-scan semi-transparent, submerged animals, and objects within seconds. To demonstrate the method, we generated full three-dimensional reconstructions (3DRs) of an object of known dimensions for verification, as well as two live marine animals-a siphonophore and an amphipod-allowing detailed measurements on each. Techniques like these pave the way for faster data capture, integrative and comparative quantitative approaches, and more accessible collections of fragile and rare biological samples.

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References

Do S, Karl W, Liang Z, Kalra M, Brady T, Pien H . A decomposition-based CT reconstruction formulation for reducing blooming artifacts. Phys Med Biol. 2011; 56(22):7109-25. DOI: 10.1088/0031-9155/56/22/008. View

Fedorov A, Beichel R, Kalpathy-Cramer J, Finet J, Fillion-Robin J, Pujol S . 3D Slicer as an image computing platform for the Quantitative Imaging Network. Magn Reson Imaging. 2012; 30(9):1323-41. PMC: 3466397. DOI: 10.1016/j.mri.2012.05.001. View

Diaz-Pinto A, Alle S, Nath V, Tang Y, Ihsani A, Asad M . MONAI Label: A framework for AI-assisted interactive labeling of 3D medical images. Med Image Anal. 2024; 95:103207. DOI: 10.1016/j.media.2024.103207. View

Irschick D, Christiansen F, Hammerschlag N, Martin J, Madsen P, Wyneken J . 3D visualization processes for recreating and studying organismal form. iScience. 2022; 25(9):104867. PMC: 9437858. DOI: 10.1016/j.isci.2022.104867. View

Cox P, Fagan M, Rayfield E, Jeffery N . Finite element modelling of squirrel, guinea pig and rat skulls: using geometric morphometrics to assess sensitivity. J Anat. 2011; 219(6):696-709. PMC: 3237878. DOI: 10.1111/j.1469-7580.2011.01436.x. View

Felice R, Tobias J, Pigot A, Goswami A . Dietary niche and the evolution of cranial morphology in birds. Proc Biol Sci. 2019; 286(1897):20182677. PMC: 6408879. DOI: 10.1098/rspb.2018.2677. View

Bagge L, Osborn K, Johnsen S . Nanostructures and Monolayers of Spheres Reduce Surface Reflections in Hyperiid Amphipods. Curr Biol. 2017; 26(22):3071-3076. DOI: 10.1016/j.cub.2016.09.033. View

Badea C, Drangova M, Holdsworth D, Johnson G . In vivo small-animal imaging using micro-CT and digital subtraction angiography. Phys Med Biol. 2008; 53(19):R319-50. PMC: 2663796. DOI: 10.1088/0031-9155/53/19/R01. View

Appeltans W, Ahyong S, Anderson G, Angel M, Artois T, Bailly N . The magnitude of global marine species diversity. Curr Biol. 2012; 22(23):2189-202. DOI: 10.1016/j.cub.2012.09.036. View

10.

Su I, Narayanan N, Logrono M, Guo K, Bisshop A, Muhlethaler R . In situ three-dimensional spider web construction and mechanics. Proc Natl Acad Sci U S A. 2021; 118(33). PMC: 8379916. DOI: 10.1073/pnas.2101296118. View

11.

Medina J, Maley J, Sannapareddy S, Medina N, Gilman C, McCormack J . A rapid and cost-effective pipeline for digitization of museum specimens with 3D photogrammetry. PLoS One. 2020; 15(8):e0236417. PMC: 7425849. DOI: 10.1371/journal.pone.0236417. View

12.

Gemmell B, Dabiri J, Colin S, Costello J, Townsend J, Sutherland K . Cool your jets: biological jet propulsion in marine invertebrates. J Exp Biol. 2021; 224(12). DOI: 10.1242/jeb.222083. View

13.

Katija K, Sherlock R, Sherman A, Robison B . New technology reveals the role of giant larvaceans in oceanic carbon cycling. Sci Adv. 2017; 3(5):e1602374. PMC: 5415331. DOI: 10.1126/sciadv.1602374. View

14.

Boyd P, Claustre H, Levy M, Siegel D, Weber T . Multi-faceted particle pumps drive carbon sequestration in the ocean. Nature. 2019; 568(7752):327-335. DOI: 10.1038/s41586-019-1098-2. View

15.

Zeidler W . A review of the hyperiidean amphipod family Brachyscelidae Stephensen, 1923 (Crustacea: Amphipoda: Hyperiidea). Zootaxa. 2021; 5026(3):405-439. DOI: 10.11646/zootaxa.5026.3.4. View

16.

Katija K, Troni G, Daniels J, Lance K, Sherlock R, Sherman A . Revealing enigmatic mucus structures in the deep sea using DeepPIV. Nature. 2020; 583(7814):78-82. DOI: 10.1038/s41586-020-2345-2. View

17.

Irigoien X, Klevjer T, Rostad A, Martinez U, Boyra G, Acuna J . Large mesopelagic fishes biomass and trophic efficiency in the open ocean. Nat Commun. 2014; 5:3271. PMC: 3926006. DOI: 10.1038/ncomms4271. View

18.

Schindelin J, Arganda-Carreras I, Frise E, Kaynig V, Longair M, Pietzsch T . Fiji: an open-source platform for biological-image analysis. Nat Methods. 2012; 9(7):676-82. PMC: 3855844. DOI: 10.1038/nmeth.2019. View

19.

Weidert S, Andress S, Linhart C, Suero E, Greiner A, Bocker W . 3D printing method for next-day acetabular fracture surgery using a surface filtering pipeline: feasibility and 1-year clinical results. Int J Comput Assist Radiol Surg. 2020; 15(3):565-575. PMC: 7973705. DOI: 10.1007/s11548-019-02110-0. View

20.

Wegst U, Bai H, Saiz E, Tomsia A, Ritchie R . Bioinspired structural materials. Nat Mater. 2014; 14(1):23-36. DOI: 10.1038/nmat4089. View