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Mitra AT, Womack MC, Gower DJ, Streicher JW, Clark B, Bell RC, Schott RK, Fujita MK, Thomas KN. Ocular lens morphology is influenced by ecology and metamorphosis in frogs and toads. Proc Biol Sci 2022; 289:20220767. [PMID: 36382525 PMCID: PMC9667364 DOI: 10.1098/rspb.2022.0767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The shape and relative size of an ocular lens affect the focal length of the eye, with consequences for visual acuity and sensitivity. Lenses are typically spherical in aquatic animals with camera-type eyes and axially flattened in terrestrial species to facilitate vision in optical media with different refractive indices. Frogs and toads (Amphibia: Anura) are ecologically diverse, with many species shifting from aquatic to terrestrial ecologies during metamorphosis. We quantified lens shape and relative size using 179 micro X-ray computed tomography scans of 126 biphasic anuran species and tested for correlations with life stage, environmental transitions, adult habits and adult activity patterns. Across broad phylogenetic diversity, tadpole lenses are more spherical than those of adults. Biphasic species with aquatic larvae and terrestrial adults typically undergo ontogenetic changes in lens shape, whereas species that remain aquatic as adults tend to retain more spherical lenses after metamorphosis. Further, adult lens shape is influenced by adult habit; notably, fossorial adults tend to retain spherical lenses following metamorphosis. Finally, lens size relative to eye size is smaller in aquatic and semiaquatic species than other adult ecologies. Our study demonstrates how ecology shapes visual systems, and the power of non-invasive imaging of museum specimens for studying sensory evolution.
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Affiliation(s)
- Amartya T. Mitra
- Division of Biosciences, University College London, London, UK
- Department of Life Sciences, The Natural History Museum, London SW7 5BD, UK
| | - Molly C. Womack
- Department of Biology, Utah State University, Logan, UT 84322, USA
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560-0162, USA
| | - David J. Gower
- Department of Life Sciences, The Natural History Museum, London SW7 5BD, UK
| | | | - Brett Clark
- Imaging and Analysis Centre, The Natural History Museum, London SW7 5BD, UK
| | - Rayna C. Bell
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560-0162, USA
- Department of Herpetology, California Academy of Sciences, San Francisco, CA 94118, USA
| | - Ryan K. Schott
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560-0162, USA
- Department of Biology and Centre for Vision Research, York University, Toronto, Ontario, Canada
| | - Matthew K. Fujita
- Department of Biology, Amphibian and Reptile Diversity Research Center, The University of Texas at Arlington, Arlington, TX 76019, USA
| | - Kate N. Thomas
- Department of Life Sciences, The Natural History Museum, London SW7 5BD, UK
- Department of Biology, Amphibian and Reptile Diversity Research Center, The University of Texas at Arlington, Arlington, TX 76019, USA
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Sena G, Fidalgo G, Paiva K, Barcelos R, Nogueira LP, Colaço MV, Gonzalez MS, Azambuja P, Colaço G, da Silva HR, de Moura Meneses AA, Barroso RC. Synchrotron X-ray biosample imaging: opportunities and challenges. Biophys Rev. [DOI: 10.1007/s12551-022-00964-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 05/25/2022] [Indexed: 12/17/2022] Open
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Paiva K, Meneses AADM, Barcellos R, Moura MSDS, Mendes G, Fidalgo G, Sena G, Colaço G, Silva HR, Braz D, Colaço MV, Barroso RC. Performance evaluation of segmentation methods for assessing the lens of the frog Thoropa miliaris from synchrotron-based phase-contrast micro-CT images. Phys Med 2022; 94:43-52. [PMID: 34995977 DOI: 10.1016/j.ejmp.2021.12.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 11/16/2021] [Accepted: 12/20/2021] [Indexed: 12/15/2022] Open
Abstract
PURPOSE In the context of synchrotron microtomography using propagation-based phase-contrast imaging (XSPCT), we evaluated the performance of semiautomatic and automatic image segmentation of soft biological structures by means of Dice Similarity Coefficient (DSC) and volume quantification. METHODS We took advantage of the phase-contrast effects of XSPCT to provide enhanced object boundaries and improved visualization of the lenses of the frog Thoropa miliaris. Then, we applied semiautomatic segmentation methods 1 and 2 (Interpolation and Watershed, respectively) and method 3, an automatic segmentation algorithm using the U-Net architecture, to the reconstructed images. DSC and volume quantification of the lenses were used to quantify the performance of image segmentation methods. RESULTS Comparing the lenses segmented by the three methods, the most pronounced difference in volume quantification was between methods 1 and 3: a reduction of 4.24%. Method 1, 2 and 3 obtained the global average DSC of 97.02%, 95.41% and 89.29%, respectively. Although it obtained the lowest DSC, method 3 performed the segmentation in a matter of seconds, while the semiautomatic methods had the average time to segment the lenses around 1 h and 30 min. CONCLUSIONS Our results suggest that the performance of U-Net was impaired due to the irregularities of the ROI edges mainly in its lower and upper regions, but it still showed high accuracy (DSC = 89.29%) with significantly reduced segmentation time compared to the semiautomatic methods. Besides, with the present work we have established a baseline for future assessments of Deep Neural Networks applied to XSPCT volumes.
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Affiliation(s)
- Katrine Paiva
- Laboratory of Applied Physics to Biomedical and Environmental Sciences, Physics Institute, State University of Rio de Janeiro, Rio de Janeiro, Brazil.
| | | | - Renan Barcellos
- Laboratory of Applied Physics to Biomedical and Environmental Sciences, Physics Institute, State University of Rio de Janeiro, Rio de Janeiro, Brazil; Nuclear Engineering Program/COPPE, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | | | - Gabriela Mendes
- Laboratory of Applied Physics to Biomedical and Environmental Sciences, Physics Institute, State University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Gabriel Fidalgo
- Laboratory of Applied Physics to Biomedical and Environmental Sciences, Physics Institute, State University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Gabriela Sena
- Nuclear Engineering Program/COPPE, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Gustavo Colaço
- Laboratory of Herpetology, Institute of Biological and Health Sciences, Federal Rural University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Hélio Ricardo Silva
- Laboratory of Herpetology, Institute of Biological and Health Sciences, Federal Rural University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Delson Braz
- Nuclear Engineering Program/COPPE, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Marcos Vinicius Colaço
- Laboratory of Applied Physics to Biomedical and Environmental Sciences, Physics Institute, State University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Regina Cely Barroso
- Laboratory of Applied Physics to Biomedical and Environmental Sciences, Physics Institute, State University of Rio de Janeiro, Rio de Janeiro, Brazil
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