Biodiversity Data Journal :
Data Paper (Biosciences)
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Corresponding author: Eva Chatzinikolaou (evachatz@hcmr.gr)
Academic editor: Vasilis Gerovasileiou
Received: 16 Sep 2021 | Accepted: 20 Nov 2021 | Published: 07 Dec 2021
© 2021 Eva Chatzinikolaou, Kleoniki Keklikoglou, Panagiotis Grigoriou, Christos Arvanitidis
This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Citation:
Chatzinikolaou E, Keklikoglou K, Grigoriou P, Arvanitidis C (2021) Micro-CT image gallery visually presenting the effects of ocean warming and acidification on marine gastropod shells. Biodiversity Data Journal 9: e75358. https://doi.org/10.3897/BDJ.9.e75358
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Digitisation of specimens (e.g. zoological, botanical) can provide access to advanced morphological and anatomical information and promote new research opportunities. The micro-CT technology may support the development of "virtual museums" or "virtual laboratories" where digital 3D imaging data are shared widely and freely. There is currently a lack of universal standards concerning the publication and curation of micro-CT datasets.
The aim of the current project was to create a virtual gallery with micro-CT scans of individuals of the marine gastropod Hexaplex trunculus, which were maintained under a combination of increased temperature and low pH conditions, thus simulating future climate change scenarios. The 3D volume-rendering models created were used to visualise the structure properties of the gastropods shells. Finally, the 3D analysis performed on the micro-CT scans was used to investigate potential changes in the shell properties of the gastropods. The derived micro-CT 3D images were annotated with detailed metadata and can be interactively displayed and manipulated using online tools through the micro-CT virtual laboratory, which was developed under the LifeWatchGreece Research Infrastructure for the dissemination of virtual image galleries collection supporting the principles of FAIR data.
micro-CT, 3D image galleries, gastropod, shell, Hexaplex trunculus, climate change, ocean acidification, ocean warming
The need for access to accurate virtual representations of species has been mentioned by several authors (
The aim of the project was to investigate the effect of ocean warming and acidification, as a result of climate change, on the shell structure of the marine gastropod Hexaplex trunculus, using a non-destructive 3D imaging technique. Furthermore, this data paper presents an example of how the micro-CT datasets can be shared and retrieved in order to contribute to the massive digitisation and open access of biological collections.
The higher levels of greenhouse gas emissions are mainly responsible for the increase observed in the global average sea surface temperature during the last 60 years (
Individuals with calcified structures are able to adjust their shell properties under ocean acidification conditions, mainly the ones related to thickness and packing (i.e. porosity) of calcium carbonate crystals, in order to build more resilient shells (
The micro-CT image datasets of the present study were stored in the Micro-CT virtual laboratory (micro-CT vLab), which is developed under the LifeWatchGreece ESFRI Research Infrastructure and supports the integration of imaging data into a large European Infrastructure. The micro-CT vLab hosts and disseminates micro-CT virtual image galleries with 3D specimens of various taxa, annotated with detailed metadata through a catalogue API service. The users are able to either retrieve the datasets or to interact with the 3D models by using a series of online tools giving the opportunity to virtually dissect the samples. All scans have been performed using a Skyscan 1172 microtomograph (Bruker, Kontich, Belgium) at the Hellenic Centre for Marine Research (HCMR). The cross-section images can be used to create 3D volume rendering images and videos of specimens. The wide dissemination of these "cyber-specimens" aims to contribute to a massive digitisation and open access of biological collections, thus contributing to the well recognised FAIR data principles.
Effects of climate change and ocean acidification on marine gastropods (ECCO project)
Dr Eva Chatzinikolaou (scientific responsible, experimental design, sample scanning, image analysis, data management), Kleoniki Keklikoglou (sample scanning, image analysis, data management), Dr Panagiotis Grigoriou (experimental design).
Mediterranean Sea, Greece, Crete
Individuals of the gastropod Hexaplex trunculus (Linnaeus, 1758) were collected from shallow (< 5 m) soft bottom habitats (Crete, Greece), acclimatised in laboratory conditions for a month and then equally separated into four different experimental treatments (55-60 individuals per treatment; size range 13.2-70.9 mm): a) Control (normal pH = 8.1 and ambient temperature, b) Acid (low pH = 7.8 and ambient temperature, c) Warm (normal pH = 8.1 and increased temperature +3ºC) and d) Warm and acid (low pH = 7.8 and increased temperature +3ºC). The experimental treatments were representing the RCP8.5 "high GHG emission" scenario according to the Intergovernmental Panel for Climate Change (
Hexaplex trunculus was selected as the model species for this experiment since it is a common and widely distributed sublittoral gastropod, which is well-adjusted to varying physical environmental conditions characterising transitional coastal systems (e.g. rock pools, lagoons) where temperature and pH fluctuations occur naturally (
This work was funded under the project ECCO (HFRI, Hellenic Foundation for Research and Innovation for the support of Post-doctoral Researchers, project ID 343).
A group of six individuals per treatment were randomly sampled for scanning in the micro-CT after the gastropods were maintained for 12 months under the experimental conditions.
One of the four experimental treatments was the Control (ambient temperature, normal pH) which serves as a quality control measure for the experimental design. Six randomly-selected replicates (specimens) were scanned from each treatment in order to adjust for any possible variability between individual gastropods. A 1:1 ratio of female:male was selected for the scanned specimens.
The following steps were followed for scanning and analysis of the selected specimens:
The parameters of the scanning, reconstruction and analysis procedure remain the same amongst the different treatments in order to obtain comparable results.
The detailed protocols for Hexaplex trunculus scanning and analysis have been published and received a DOI under https://dx.doi.org/10.17504/protocols.io.bxwqppdw.
The collection of samples was performed in Elounda, Crete, Greece (N 35° 16' 2.4'', E 25° 43' 27.2'').
Phylum: Mollusca, Class: Gastropoda, Order: Neogastropoda, Family: Muricidae, Genus: Hexaplex, Species: Hexaplex trunculus
Non-applicable.
The dataset is available through the Micro-CT vLab hosted in the Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC) of the Hellenic Centre for Marine Research (HCMR). The current publication aims to describe the 3D image galleries produced during the micro-CT scanning of specimens derived from the four ECCO project experimental treatments: 1) Hexaplex trunculus in normal conditions (https://microct.portal.lifewatchgreece.eu/node/70), 2) Hexaplex trunculus in acidified conditions (https://microct.portal.lifewatchgreece.eu/node/69), 3) Hexaplex trunculus in warm conditions (https://microct.portal.lifewatchgreece.eu/node/71) and 4) Hexaplex trunculus in warm and acidified conditions (https://microct.portal.lifewatchgreece.eu/node/72). These four galleries (i.e. "Hexaplex trunculus projects") are freely available for downloading and online manipulation through the LifeWatchGreece web portal interface.
The micro-CT gallery for each "project" includes a General Info tab (Fig.
In the 3D visualisation tab, a "volume" slider appears on the upper left side of the panel, which enables the display of the selected micro-CT dataset either as 2D or 3D using the Slice:Drop software. The user can explore the micro-CT dataset in 2D and view all the micro-CT slices in three orthogonal views (x, y, z axes) (Fig.
The Video tab displays a short preview video as a demonstration of the specific micro-CT dataset (Fig.
The Metadata tab contains complete detailed information about the dataset, the pre-scanning procedures and the scanning parameters, following the schema proposed by
Table: Metadata terms of micro-CT vLab datasets and their definitions.
Column label | Column description |
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Specimen ID | A unique identifier for the specimen in the format mCT-xxxxx (where x = incrementing number from 00001 to 99999, with preceding zeros). |
Scan ID | A unique code of the format scan-xxxxx (where x = incrementing number from 00001 to 99999, with preceding zeros). |
Sample Category | The category to which the specimen belongs, for example, Zoology, Botany. |
Scientific name | The lowest taxonomic name to which the specimen has been identified. |
Taxonomic Group | The general taxonomic group to which the specimen belongs, for example, Polychaeta, Insecta |
Specimen Description | A verbatim description of the specimen, which allows the understanding of the nature of the specimen at a glance. |
Provider Institute | Institution (i.e. academic, scientific) which provided the specimen. |
Specimen Provider | Name of the person who provided the specimen. |
Material | The material of the scanned sample, for example, soft tissue. |
Fixation Type | Type of chemical used for the fixation of the specimen, for example, formalin. |
Preservation Medium | Means used for preservation of the specimen, for example, ethanol, freezer. |
Contrast Enhancement Method | Contrast agent (short name of the chemical, for example, PTA) used in order to achieve contrast difference between the specimen and its surrounding medium. |
Scope of Scan | Reason for performing a scan. |
Scan date | Start date of the scanning in the format MM/DD/YYYY. |
Scanned By | The name of the person who performed the scan. |
Sample Holder | A description of the sample holder, for example, pipette tip. |
Scanning Medium | The medium that surrounds the sample during scanning, for example, air, ethanol. |
Scanned Part | The part of the specimen that has been scanned, for example, anterior part, full specimen. |
Digital Device Type | The brand (manufacturer) of the Digital Device that was used for the scanning. |
Voltage kV | The voltage of scanning in kilovolt (kV). |
Current μA | The current of scanning in μAmpere. |
Filter | The type of the filter that is used for scanning, for example, Aluminium |
Zoom (μm) | The resolution of the scan in μm (zoom level), for example, 1.24. |
Camera Resolution | Camera resolution settings in pixels, for example, 4000. |
Exposure Time (ms) | Duration of time (milliseconds) the sample is exposed under X-rays. |
360 | Full (360°) or half (180°) rotation of the specimen during scanning. |
Random Movement | The maximum number of pixels to randomly move the specimen up and down in order to avoid "dead pixels". |
Averaging | The number of images acquired for each position (angle) in order to estimate the frame averaging value. |
Oversize Settings | The number of parts (vertical & horizontal) used for scanning of oversize specimens. |
Dataset | Download the dataset in NIfTI format. |
Micro-CT Images | Download the micro-CT images. |
Video File | Download the micro-CT video in mp4. |
This work was funded under the project ECCO (HFRI, Hellenic Foundation for Research and Innovation for the support of Post-doctoral Researchers, project ID 343). The development of the micro-CT vLab was supported by the projects: a) LifeWatchGreece Infrastructure (ESFRI, MIS 384676) funded by GSRT/NSRF, b) ELIXIR-GR: Managing and Analysing Life Sciences Data (MIS: 5002780) co-financed by Greece and the European Union - European Regional Development Fund, c) BIOIMAGING‐GR (MIS 5002755) implemented under “Action for Strengthening Research and Innovation Infrastructures”, funded by the Operational Programme “Competitiveness, Entrepreneurship and Innovation” (NSRF 2014–2020) and co‐financed by Greece and the European Union (European Regional Development Fund), d) ENVRI FAIR (Horizon H2020, Grand Agreement 824068) and e) SYNTHESYS PLUS (Horizon H2020, Grand Agreement 823827).
Dr Eva Chatzinikolaou (writing of manuscript, experimental design, design of scanning protocols, implementation of scanning and 3D analysis, project scientific responsible, funding acquisition)
Kleoniki Keklikoglou (writing of manuscript, design of scanning protocols, implementation of scanning and 3D analysis)
Dr Panagiotis Grigoriou (writing of manuscript, experimental design)
Dr Christos Arvanitidis (writing of manuscript, support on micro-CT vLab development)