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dc.contributor.authorTills, O
dc.contributor.authorSpicer, JI
dc.contributor.authorGrimmer, A
dc.contributor.authorMarini, S
dc.contributor.authorJie, VW
dc.contributor.authorTully, E
dc.contributor.authorRundle, SD
dc.contributor.editorBaden T
dc.date.accessioned2019-01-22T18:41:02Z
dc.date.available2019-01-22T18:41:02Z
dc.date.issued2018
dc.identifier.issn1544-9173
dc.identifier.issn1545-7885
dc.identifier.othere3000074
dc.identifier.urihttp://hdl.handle.net/10026.1/13214
dc.description.abstract

Phenomics has the potential to facilitate significant advances in biology but requires the development of high-throughput technologies capable of generating and analysing high-dimensional data. There are significant challenges associated with building such technologies, not least those required for investigating dynamic processes such as embryonic development, during which high rates of temporal, spatial, and functional change are inherently difficult to capture. Here, we present EmbryoPhenomics, an accessible high-throughput platform for phenomics in aquatic embryos comprising an Open-source Video Microscope (OpenVIM) that produces high-resolution videos of multiple embryos under tightly controlled environmental conditions. These videos are then analysed by the Python package Embryo Computer Vision (EmbryoCV), which extracts phenomic data for morphological, physiological, behavioural, and proxy traits during the process of embryonic development. We demonstrate the broad-scale applicability of EmbryoPhenomics in a series of experiments assessing chronic, acute, and multistressor responses to environmental change (temperature and salinity) in >30 million images of >600 embryos of two species with markedly different patterns of development-the pond snail Radix balthica and the marine amphipod Orchestia gammarellus. The challenge of phenomics is significant but so too are the rewards, and it is particularly relevant to the urgent task of assessing complex organismal responses to current rates of environmental change. EmbryoPhenomics can acquire and process data capturing functional, temporal, and spatial responses in the earliest, most dynamic life stages and is potentially game changing for those interested in studying development and phenomics more widely.

dc.format.extente3000074-e3000074
dc.format.mediumElectronic-eCollection
dc.languageen
dc.language.isoen
dc.publisherPublic Library of Science (PLoS)
dc.subjectAnimals
dc.subjectBiological Variation, Population
dc.subjectEmbryonic Development
dc.subjectHigh-Throughput Screening Assays
dc.subjectHumans
dc.subjectMicroscopy, Video
dc.subjectPhenotype
dc.titleA high-throughput and open-source platform for embryo phenomics
dc.typejournal-article
dc.typeArticle
plymouth.author-urlhttps://www.ncbi.nlm.nih.gov/pubmed/30543636
plymouth.issue12
plymouth.volume16
plymouth.publisher-urlhttp://dx.doi.org/10.1371/journal.pbio.3000074
plymouth.publication-statusPublished online
plymouth.journalPLOS Biology
dc.identifier.doi10.1371/journal.pbio.3000074
plymouth.organisational-group/Plymouth
plymouth.organisational-group/Plymouth/Admin Group - REF
plymouth.organisational-group/Plymouth/Admin Group - REF/REF Admin Group - FoSE
plymouth.organisational-group/Plymouth/Faculty of Science and Engineering
plymouth.organisational-group/Plymouth/Faculty of Science and Engineering/School of Biological and Marine Sciences
plymouth.organisational-group/Plymouth/REF 2021 Researchers by UoA
plymouth.organisational-group/Plymouth/REF 2021 Researchers by UoA/UoA07 Earth Systems and Environmental Sciences
plymouth.organisational-group/Plymouth/Research Groups
plymouth.organisational-group/Plymouth/Research Groups/Marine Institute
plymouth.organisational-group/Plymouth/Users by role
plymouth.organisational-group/Plymouth/Users by role/Academics
plymouth.organisational-group/Plymouth/Users by role/Researchers in ResearchFish submission
dc.publisher.placeUnited States
dcterms.dateAccepted2018-01-01
dc.rights.embargodate2021-11-27
dc.identifier.eissn1545-7885
dc.rights.embargoperiodNot known
rioxxterms.versionofrecord10.1371/journal.pbio.3000074
rioxxterms.licenseref.urihttp://www.rioxx.net/licenses/all-rights-reserved
rioxxterms.typeJournal Article/Review
plymouth.funderDevelopment of an automated analytical system for measurement of whole-organism environmental sensitivity of aquatic embryos::NERC


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