Loading…
Using 3D micro-geomorphometry to quantify interstitial spaces of an oyster cluster
In ecology, it is assumed that the characteristics (e.g. shape, size) of interstitial spaces found in a variety of habitats affect the colonization of species, species interactions, and species composition. However, those characteristics have traditionally been difficult to measure due to technologi...
Saved in:
Published in: | PeerJ preprints 2019-03 |
---|---|
Main Authors: | , , |
Format: | Article |
Language: | English |
Subjects: | |
Citations: | Items that cite this one |
Online Access: | Get full text |
Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
cited_by | cdi_FETCH-LOGICAL-c1311-d2939f5bf17ad7b90964de23e12373d72edd64a4a6cf547fd19ac060609715503 |
---|---|
cites | |
container_end_page | |
container_issue | |
container_start_page | |
container_title | PeerJ preprints |
container_volume | |
creator | Kim, Kwanmok Lecours, Vincent Frederick, Peter C |
description | In ecology, it is assumed that the characteristics (e.g. shape, size) of interstitial spaces found in a variety of habitats affect the colonization of species, species interactions, and species composition. However, those characteristics have traditionally been difficult to measure due to technological limitations. In this study, we used the Structure-from-Motion (SfM) photogrammetry technique to measure the physical characteristics of interstitial spaces in a small oyster cluster. The point cloud (and mesh) of the oyster cluster derived from SfM photogrammetry was found to be accurate enough (mean error of 0.654 mm) to conduct 3D geomorphometric analyses. We present an example of measures of curvature, roughness, interstitial volume, surface area, and openness for three 3D interstitial spaces. The interpretation of those measures enabled establishing which interstitial spaces were the most likely to be used as a shelter for an average crab. Those spaces are characterized by smaller openness and higher roughness and curvature measures. This initial quantitative 3D characterization of an oyster cluster is the first step in establishing empirical relationships between structural complexity of biological structures like oyster clusters and their ecological role for instance in predator-prey interactions. Overall, this study demonstrates the feasibility of combining SfM photogrammetry with geomorphometry for fine-scale ecological studies. |
doi_str_mv | 10.7287/peerj.preprints.27596v1 |
format | article |
fullrecord | <record><control><sourceid>proquest</sourceid><recordid>TN_cdi_proquest_journals_2193450949</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><sourcerecordid>2193450949</sourcerecordid><originalsourceid>FETCH-LOGICAL-c1311-d2939f5bf17ad7b90964de23e12373d72edd64a4a6cf547fd19ac060609715503</originalsourceid><addsrcrecordid>eNotjctKAzEARYMgWGq_wYDrGfNOs5T6hIIgdl3SPGqGmUmaZIT-vSOWuziLC-cAcIdRK8laPiTnctem7FIOYy0tkVyJH3wFFgQL2ag1ozdgVUqHEMKECyLVAnzuShiPkD7BIZgcm6OLQ8zpOw6u5jOsEZ4mPdbgz3CWulxqqEH3sCRtXIHRQz3CeC7zBU0__fEWXHvdF7e6cAl2L89fm7dm-_H6vnncNgZTjBtLFFWeHzyW2sqDQkow6wh1mFBJrSTOWsE008J4zqS3WGmDxDwlMeeILsH9vzfleJpcqfsuTnmck3uCFWUcKaboL1jSVWQ</addsrcrecordid><sourcetype>Aggregation Database</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>2193450949</pqid></control><display><type>article</type><title>Using 3D micro-geomorphometry to quantify interstitial spaces of an oyster cluster</title><source>Publicly Available Content Database</source><creator>Kim, Kwanmok ; Lecours, Vincent ; Frederick, Peter C</creator><creatorcontrib>Kim, Kwanmok ; Lecours, Vincent ; Frederick, Peter C</creatorcontrib><description>In ecology, it is assumed that the characteristics (e.g. shape, size) of interstitial spaces found in a variety of habitats affect the colonization of species, species interactions, and species composition. However, those characteristics have traditionally been difficult to measure due to technological limitations. In this study, we used the Structure-from-Motion (SfM) photogrammetry technique to measure the physical characteristics of interstitial spaces in a small oyster cluster. The point cloud (and mesh) of the oyster cluster derived from SfM photogrammetry was found to be accurate enough (mean error of 0.654 mm) to conduct 3D geomorphometric analyses. We present an example of measures of curvature, roughness, interstitial volume, surface area, and openness for three 3D interstitial spaces. The interpretation of those measures enabled establishing which interstitial spaces were the most likely to be used as a shelter for an average crab. Those spaces are characterized by smaller openness and higher roughness and curvature measures. This initial quantitative 3D characterization of an oyster cluster is the first step in establishing empirical relationships between structural complexity of biological structures like oyster clusters and their ecological role for instance in predator-prey interactions. Overall, this study demonstrates the feasibility of combining SfM photogrammetry with geomorphometry for fine-scale ecological studies.</description><identifier>EISSN: 2167-9843</identifier><identifier>DOI: 10.7287/peerj.preprints.27596v1</identifier><language>eng</language><publisher>San Diego: PeerJ, Inc</publisher><subject>Colonization ; Physical characteristics ; Predator-prey interactions ; Prey ; Species composition</subject><ispartof>PeerJ preprints, 2019-03</ispartof><rights>2019 Kim et al. This is an open access article distributed under the terms of the Creative Commons Attribution License: http://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ Preprints) and either DOI or URL of the article must be cited. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c1311-d2939f5bf17ad7b90964de23e12373d72edd64a4a6cf547fd19ac060609715503</citedby></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktohtml>$$Uhttps://www.proquest.com/docview/2193450949?pq-origsite=primo$$EHTML$$P50$$Gproquest$$Hfree_for_read</linktohtml><link.rule.ids>314,780,784,25752,27923,27924,37011,44589</link.rule.ids></links><search><creatorcontrib>Kim, Kwanmok</creatorcontrib><creatorcontrib>Lecours, Vincent</creatorcontrib><creatorcontrib>Frederick, Peter C</creatorcontrib><title>Using 3D micro-geomorphometry to quantify interstitial spaces of an oyster cluster</title><title>PeerJ preprints</title><description>In ecology, it is assumed that the characteristics (e.g. shape, size) of interstitial spaces found in a variety of habitats affect the colonization of species, species interactions, and species composition. However, those characteristics have traditionally been difficult to measure due to technological limitations. In this study, we used the Structure-from-Motion (SfM) photogrammetry technique to measure the physical characteristics of interstitial spaces in a small oyster cluster. The point cloud (and mesh) of the oyster cluster derived from SfM photogrammetry was found to be accurate enough (mean error of 0.654 mm) to conduct 3D geomorphometric analyses. We present an example of measures of curvature, roughness, interstitial volume, surface area, and openness for three 3D interstitial spaces. The interpretation of those measures enabled establishing which interstitial spaces were the most likely to be used as a shelter for an average crab. Those spaces are characterized by smaller openness and higher roughness and curvature measures. This initial quantitative 3D characterization of an oyster cluster is the first step in establishing empirical relationships between structural complexity of biological structures like oyster clusters and their ecological role for instance in predator-prey interactions. Overall, this study demonstrates the feasibility of combining SfM photogrammetry with geomorphometry for fine-scale ecological studies.</description><subject>Colonization</subject><subject>Physical characteristics</subject><subject>Predator-prey interactions</subject><subject>Prey</subject><subject>Species composition</subject><issn>2167-9843</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2019</creationdate><recordtype>article</recordtype><sourceid>PIMPY</sourceid><recordid>eNotjctKAzEARYMgWGq_wYDrGfNOs5T6hIIgdl3SPGqGmUmaZIT-vSOWuziLC-cAcIdRK8laPiTnctem7FIOYy0tkVyJH3wFFgQL2ag1ozdgVUqHEMKECyLVAnzuShiPkD7BIZgcm6OLQ8zpOw6u5jOsEZ4mPdbgz3CWulxqqEH3sCRtXIHRQz3CeC7zBU0__fEWXHvdF7e6cAl2L89fm7dm-_H6vnncNgZTjBtLFFWeHzyW2sqDQkow6wh1mFBJrSTOWsE008J4zqS3WGmDxDwlMeeILsH9vzfleJpcqfsuTnmck3uCFWUcKaboL1jSVWQ</recordid><startdate>20190318</startdate><enddate>20190318</enddate><creator>Kim, Kwanmok</creator><creator>Lecours, Vincent</creator><creator>Frederick, Peter C</creator><general>PeerJ, Inc</general><scope>3V.</scope><scope>7XB</scope><scope>88I</scope><scope>8FE</scope><scope>8FH</scope><scope>8FK</scope><scope>ABUWG</scope><scope>AFKRA</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BHPHI</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>GNUQQ</scope><scope>HCIFZ</scope><scope>LK8</scope><scope>M2P</scope><scope>M7P</scope><scope>PIMPY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PRINS</scope><scope>Q9U</scope></search><sort><creationdate>20190318</creationdate><title>Using 3D micro-geomorphometry to quantify interstitial spaces of an oyster cluster</title><author>Kim, Kwanmok ; Lecours, Vincent ; Frederick, Peter C</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c1311-d2939f5bf17ad7b90964de23e12373d72edd64a4a6cf547fd19ac060609715503</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2019</creationdate><topic>Colonization</topic><topic>Physical characteristics</topic><topic>Predator-prey interactions</topic><topic>Prey</topic><topic>Species composition</topic><toplevel>online_resources</toplevel><creatorcontrib>Kim, Kwanmok</creatorcontrib><creatorcontrib>Lecours, Vincent</creatorcontrib><creatorcontrib>Frederick, Peter C</creatorcontrib><collection>ProQuest Central (Corporate)</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Science Database (Alumni Edition)</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>ProQuest Central (Alumni) (purchase pre-March 2016)</collection><collection>ProQuest Central (Alumni)</collection><collection>ProQuest Central</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>AUTh Library subscriptions: ProQuest Central</collection><collection>ProQuest Natural Science Collection</collection><collection>ProQuest One Community College</collection><collection>ProQuest Central</collection><collection>ProQuest Central Student</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Biological Science Collection</collection><collection>Science Database</collection><collection>Biological Science Database</collection><collection>Publicly Available Content Database</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>ProQuest Central China</collection><collection>ProQuest Central Basic</collection><jtitle>PeerJ preprints</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Kim, Kwanmok</au><au>Lecours, Vincent</au><au>Frederick, Peter C</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Using 3D micro-geomorphometry to quantify interstitial spaces of an oyster cluster</atitle><jtitle>PeerJ preprints</jtitle><date>2019-03-18</date><risdate>2019</risdate><eissn>2167-9843</eissn><abstract>In ecology, it is assumed that the characteristics (e.g. shape, size) of interstitial spaces found in a variety of habitats affect the colonization of species, species interactions, and species composition. However, those characteristics have traditionally been difficult to measure due to technological limitations. In this study, we used the Structure-from-Motion (SfM) photogrammetry technique to measure the physical characteristics of interstitial spaces in a small oyster cluster. The point cloud (and mesh) of the oyster cluster derived from SfM photogrammetry was found to be accurate enough (mean error of 0.654 mm) to conduct 3D geomorphometric analyses. We present an example of measures of curvature, roughness, interstitial volume, surface area, and openness for three 3D interstitial spaces. The interpretation of those measures enabled establishing which interstitial spaces were the most likely to be used as a shelter for an average crab. Those spaces are characterized by smaller openness and higher roughness and curvature measures. This initial quantitative 3D characterization of an oyster cluster is the first step in establishing empirical relationships between structural complexity of biological structures like oyster clusters and their ecological role for instance in predator-prey interactions. Overall, this study demonstrates the feasibility of combining SfM photogrammetry with geomorphometry for fine-scale ecological studies.</abstract><cop>San Diego</cop><pub>PeerJ, Inc</pub><doi>10.7287/peerj.preprints.27596v1</doi><oa>free_for_read</oa></addata></record> |
fulltext | fulltext |
identifier | EISSN: 2167-9843 |
ispartof | PeerJ preprints, 2019-03 |
issn | 2167-9843 |
language | eng |
recordid | cdi_proquest_journals_2193450949 |
source | Publicly Available Content Database |
subjects | Colonization Physical characteristics Predator-prey interactions Prey Species composition |
title | Using 3D micro-geomorphometry to quantify interstitial spaces of an oyster cluster |
url | http://sfxeu10.hosted.exlibrisgroup.com/loughborough?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2025-01-09T02%3A18%3A59IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-proquest&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Using%203D%20micro-geomorphometry%20to%20quantify%20interstitial%20spaces%20of%20an%20oyster%20cluster&rft.jtitle=PeerJ%20preprints&rft.au=Kim,%20Kwanmok&rft.date=2019-03-18&rft.eissn=2167-9843&rft_id=info:doi/10.7287/peerj.preprints.27596v1&rft_dat=%3Cproquest%3E2193450949%3C/proquest%3E%3Cgrp_id%3Ecdi_FETCH-LOGICAL-c1311-d2939f5bf17ad7b90964de23e12373d72edd64a4a6cf547fd19ac060609715503%3C/grp_id%3E%3Coa%3E%3C/oa%3E%3Curl%3E%3C/url%3E&rft_id=info:oai/&rft_pqid=2193450949&rft_id=info:pmid/&rfr_iscdi=true |