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14 results for “Coastal oceanography”
Organic and inorganic data for soil cores from Brazil and Florida Bay seagrasses to support Howard et al 2018, CO2 released by carbonate sediment production in some coastal areas may offset the benefits of seagrass “Blue Carbon” storage, Limnology and Oceanography, DOI: 10.1002/lno.10621
Using piston corers, soils from Florida Bay and Brazilian seagrass meadows were collected to complete organic and inorganic carbon inventories for the top 1 m of soil. Instrumental analyses and loss on ignition at 500C were used to measure C content of downcore slices.
Supplementary dataset to the publication "Bi, S., and Hieronymi, M. (2024). Holistic optical water type classification for ocean, coastal, and inland waters. Limnology & Oceanography"
<p>The NetCDF data files contain the training dataset used to develop the Optical Water Type (OWT) framework proposed by Bi and Hieronymi (2024). The dataset is available in two spectral versions:</p> <p> 1. <code>owt_BH2024_training_data_hyper.nc</code>: This file includes training data with a spectral resolution of 2 nm, ranging from 400 to 900 nm.<br> 2. <code>owt_BH2024_training_data_olci.nc</code>: This file contains data formatted similarly to the hyperspectral version but aligned with the nominal Sentinel-3 OLCI wavebands.</p> <h2>Contents of the Dataset</h2> <p>For each version, the dataset includes spectral inherent and apparent optical properties such as:</p> <p> • Remote Sensing Reflectance (Rrs)<br> • Pure Water Absorption (aw)<br> • Absorption Coefficient of Detritus (ad)<br> • Total Absorption Coefficient without Pure Water (agp)<br> • Absorption Coefficient of Phytoplankton (aph)<br> • Backscattering Coefficient of Total Particulate Matter (bbp)<br> • Scattering Coefficient of Total Particulate Matter (bp)<br> • Scattering Coefficient of Pure Water (bw)</p> <p>Additionally, the dataset includes various environmental and biological parameters:</p> <p> • Chlorophyll a Concentration (Chl)<br> • Inorganic Suspended Matter Concentration (ISM)<br> • Colored Dissolved Organic Matter Absorption at 440 nm (ag440)<br> • Single-Scattering Albedo of Detritus at 550 nm (A_d)<br> • Power Law Exponent of Detritus Attenuation (G_d)<br> • Water Salinity (Sal)<br> • Water Temperature (Temp)<br> • Fraction for Diminished Coccolithophore Absorption (a_frac)<br> • Fraction of Coccolithophore Group (cocco_frac)</p> <h2>Optical Water Types</h2> <p>The training dataset includes 10 pre-defined optical water types, with 10,000 samples for each type. Detailed descriptions of these water types can be found in Table 1 of Bi and Hieronymi (2024) or as follows,</p> <table> <tbody> <tr> <td>OWT</td> <td>Desciption</td> </tr> <tr> <td>1</td> <td>Extremely clear and oligotrophic indigo-blue waters with high reflectance in the short visible wavelengths.</td> </tr> <tr> <td>2</td> <td>Blue waters with similar biomass level as OWT 1 but with slightly higher detritus and CDOM content.</td> </tr> <tr> <td>3a</td> <td>Turquoise waters with slightly higher phytoplankton, detritus, and CDOM compared to the first two types.</td> </tr> <tr> <td>3b</td> <td>A special case of OWT 3a with similar detritus and CDOM distribution but with strong scattering and little absorbing particles like in the case of Coccolithophore blooms. This type usually appears brighter and exhibits a remarkable ~490 nm reflectance peak.</td> </tr> <tr> <td>4a</td> <td>Greenish water found in coastal and inland environments, with higher biomass compared to the previous water types. Reflectance in short wavelengths is usually depressed by the absorption of particles and CDOM.</td> </tr> <tr> <td>4b</td> <td>A special case of OWT 4a, sharing similar detritus and CDOM distribution, exhibiting phytoplankton blooms with higher scattering coefficients, e.g., Coccolithophore bloom. The color of this type shows a very bright green.</td> </tr> <tr> <td>5a</td> <td>Green eutrophic water, with significantly higher phytoplankton biomass, exhibiting a bimodal reflectance shape with typical peaks at ~560 and ~709 nm.</td> </tr> <tr> <td>5b</td> <td>Green hyper-eutrophic water, with even higher biomass than that of OWT 5a (over several orders of magnitude), displaying a reflectance plateau in the Near Infrared Region, NIR (vegetation-like spectrum).</td> </tr> <tr> <td>6</td> <td>Bright brown water with high detritus concentrations, which has a high reflectance determined by scattering.</td> </tr> <tr> <td>7</td> <td>Dark brown to black water with very high CDOM concentration, which has low reflectance in the entire visible range and is dominated by absorption.</td> </tr> </tbody> </table> <h2>Additional Information</h2> <p>The detailed description of the data simulation can be found in the supporting information of Bi and Hieronymi (2024). The models used for simulating the data are available on GitHub:</p> <p> • Component IOP Model: <a href="https://github.com/bishun945/IOPmodel" target="_blank" rel="noopener">Bio-geo-optical modelling of natural waters by Bi, Hieronymi, and Röttgers (2023)</a><br> • OWT Package: <a href="https://github.com/bishun945/pyOWT" target="_blank" rel="noopener">pyOWT</a></p> <h2>References</h2> <p> 1. OWT Framework: Bi, S., and Hieronymi, M. (2024). Holistic optical water type classification for ocean, coastal, and inland waters. Limnology & Oceanography, lno.12606. doi: 10.1002/lno.12606<br> 2. Component IOP Model: Bi, S., Hieronymi, M., and Röttgers, R. (2023). Bio-geo-optical modelling of natural waters. Front. Mar. Sci. 10, 1196352. doi: 10.3389/fmars.2023.1196352<br> 3. Pure Water IOP Model: Röttgers, R., Doerffer, R., McKee, D., and Schönfeld, W. (2016). The Water Optical Properties Processor (WOPP): Pure Water Spectral Absorption, Scattering and Real Part of Refractive Index Model. Technical Report No WOPP-ATBD/WRD6. Available at: https://calvalportal.ceos.org/tools<br> 4. Rrs Model: Lee, Z., Du, K., Voss, K. J., Zibordi, G., Lubac, B., Arnone, R., et al. (2011). An inherent-optical-property-centered approach to correct the angular effects in water-leaving radiance. Appl. Opt. 50, 3155. doi: 10.1364/AO.50.003155</p> <h2>Authors and Contact</h2> <p> • Author: Shun Bi, Martin Hieronymi, Rüdiger Röttgers<br> • Creator: Shun Bi, Shun.Bi@hereon.de</p> <h2>Example Python Code to Read Data</h2> <p>Here is an example of how to read the NetCDF data using Python and the <code>xarray</code> library:</p> <pre><code>import xarray as xr # Load the dataset data_hyper = xr.open_dataset("path_to_your_file/owt_BH2024_training_data_hyper.nc") # Print the dataset to see its structure print(data_hyper) # Access a specific variable, e.g., remote sensing reflectance (Rrs) rrs = data_hyper['Rrs'] # Plot a sample of Rrs import matplotlib.pyplot as plt # Select a sample ID, for example the first sample sample_id = 0 plt.plot(data_hyper['wavelen'], rrs[sample_id, :]) plt.xlabel('Wavelength (nm)') plt.ylabel('Rrs (1/sr)') plt.title(f'Remote Sensing Reflectance for Sample ID {sample_id}') plt.show()</code></pre>
Figure 12 in Calanoides natalis Brady, 1914 (Copepoda: Calanoida: Calanidae): identity and distribution in relation to coastal oceanography of the eastern Atlantic and western Indian Oceans
Figure 12. Relationship between greatest width and posterior width (µm) of the female genital double-somite in dorsal view for Calanoides natalis (star = Arabian Sea, diamond = off Namibia), Calanoides carinatus (square) and Calanoides brevicornis = Calanoides macrocarinatus (open circle).
Figure 11 in Calanoides natalis Brady, 1914 (Copepoda: Calanoida: Calanidae): identity and distribution in relation to coastal oceanography of the eastern Atlantic and western Indian Oceans
Figure 11. Variability in distal part of left leg 5 of Calanoides natalis: (a–d) from off Namibia; (e–i) from the Arabian Sea. Note specimen (g) has stout outer distal spine on segment 2 and many other specimens have this spine attenuated and apparently easily broken e.g. (d) and (i).
Figure 10 in Calanoides natalis Brady, 1914 (Copepoda: Calanoida: Calanidae): identity and distribution in relation to coastal oceanography of the eastern Atlantic and western Indian Oceans
Figure 10. Calanoides natalis male: (a) antennule ancestral segments I–XVII; (b) antennule ancestral segments XVIII–XXVIII; (c) antennule ancestral segments XXVII–XXVIII, setal numbers refer to numbering system of Weatherby et al. (1994); (d) antennule ancestral segments X and XI; (e) antenna; (f) mandible; (g) maxillule; (h) maxilla; (i) maxilliped; (j, k) maxilliped syncoxae from Benguela Current. Scale bars 0.1 mm.
Figure 6 in Calanoides natalis Brady, 1914 (Copepoda: Calanoida: Calanidae): identity and distribution in relation to coastal oceanography of the eastern Atlantic and western Indian Oceans
Figure 6. Calanoides natalis female: (a) quadrithek antennule, ancestral segments I–XIX; (b) quadrithek antennule, ancestral segments XX–XXVIII; (c) quadrithek antennule, ancestral segments X–XI; (d) quadrithek antennule, ancestral segments XXVII–XXVIII; (e) trithek antennule segments I–XI; (f) trithek antennule, ancestral segment XXIII; (g) antenna. a – aesthetacs; pa – pseudoannulate seta; va – vestigial aesthetasc. Scale bars represent 0.1 mm.
Figure 7 in Calanoides natalis Brady, 1914 (Copepoda: Calanoida: Calanidae): identity and distribution in relation to coastal oceanography of the eastern Atlantic and western Indian Oceans
Figure 7. Calanoides natalis female: (a) mandible; (b) maxillule; (c) maxilla; (d) maxilliped. Scale bar represents 0.1 mm.
Figure 5 in Calanoides natalis Brady, 1914 (Copepoda: Calanoida: Calanidae): identity and distribution in relation to coastal oceanography of the eastern Atlantic and western Indian Oceans
Figure 5. Calanoides natalis female: (a) dorsal view; (b) lateral view; (c) antennule; (d) genital doublesomite, lateral view; (e) genital double somite, dorsal view; (f) genital operculum (go) and left seminal receptacle (sr); (g) caudal ramus ventral view; (h) anterior head, ventral view. Scale bars represent 1.0 mm on figures (a–c) and 0.1 mm on the rest.
Figure 3. Calanoides male leg 5 in Calanoides natalis Brady, 1914 (Copepoda: Calanoida: Calanidae): identity and distribution in relation to coastal oceanography of the eastern Atlantic and western Indian Oceans
Figure 3. Calanoides male leg 5 indicating the measurements made, from which the ratios in Table 4 were calculated. (A) Length of distal spine on right exopod segment 3; (B) length of right exopod segment 3 measured along inner border; (b) width of right exopod segment 3 measured at its widest part; (C) length of right exopod segment 2 measured along inner border; (D) length of right exopod segment 1 measured along inner border; (E) total length of right endopod; (A') length of terminal spine on left exopod segment 3; (B') length of left exopod segment 3 measured along inner border; (b') width of left exopod segment 3 measured at its widest part; (C') length of left exopod segment 2 measured along inner border; (c') width of left exopod segment 2 measured at its widest part; (F) length of left exopod segment 3 measured along outer border; (G) length of outer distal spine on left exopod segment 2; (H) distance between proximal border of left exopod 3 and base of lateroproximal spine of exopod segment 3.
Figure 9 in Calanoides natalis Brady, 1914 (Copepoda: Calanoida: Calanidae): identity and distribution in relation to coastal oceanography of the eastern Atlantic and western Indian Oceans
Figure 9. Calanoides natalis male: (a) dorsal view; (b) lateral view – note specimen laterally compressed c.f. Figure 8; (c) antennule; (d) anterior head, lateral view; (e) left caudal ramus, dorsal view; (f) leg 5, posterior view; (g) left leg 5 exopod segment 3. Scale mark 1.0 mm on figures a–d, 0.1 mm on rest.
Figure 4 in Calanoides natalis Brady, 1914 (Copepoda: Calanoida: Calanidae): identity and distribution in relation to coastal oceanography of the eastern Atlantic and western Indian Oceans
Figure 4. Bayesian tree obtained from COI molecular data. Individuals are collapsed to species. Values at nodes indicate posterior probability. Monophyletic Neocalanus spp. and Mesocalanus tenuicornis were included as topology constraints. All species described in this paper were recovered as monophyletic.
Figure 2 in Calanoides natalis Brady, 1914 (Copepoda: Calanoida: Calanidae): identity and distribution in relation to coastal oceanography of the eastern Atlantic and western Indian Oceans
Figure 2. Location diagram of samples examined or mentioned in the test (see Table 1). □ – Calanoides acutus; ◊ – Calanoides brevicornis; ♦ – Calanoides carinatus s.s.; ○ – Calanoides natalis; ■ – Calanoides patagoniensis; ● – Calanoides philippinensis.
Figure 8 in Calanoides natalis Brady, 1914 (Copepoda: Calanoida: Calanidae): identity and distribution in relation to coastal oceanography of the eastern Atlantic and western Indian Oceans
Figure 8. Calanoides natalis female: (a) Leg 1 coxa, basis and endopod; (b) leg 1 exopod; (c) leg 2, anterior surface; (d) leg 3, posterior surface; (e) leg 4, posterior surface; (f) leg 5, anterior surface. Scale bar represents 0.1 mm.
Figure 1 in Calanoides natalis Brady, 1914 (Copepoda: Calanoida: Calanidae): identity and distribution in relation to coastal oceanography of the eastern Atlantic and western Indian Oceans
Figure 1. Photomicrographs of whole female (a–d) specimens in lateral view with antennules removed, and male (e) of: (a) Calanoides brevicornis (= Calanoides macrocarinatus) from 250–500 m, 42.41° S, 174.03° E; (b) Calanoides carinatus from 0–10 m, 43.67° S, 64.97° W; (c) Calanoides natalis from surface waters, Arabian Sea, 20.22° N, 58.75° E; (d) Calanoides philippinensis lateral view, Aru Basin, about 6° S, 133.5° E; (e) C. natalis from the Arabian Sea 20.22° N, 58.75° E. The Calanoides carinatus photo was made available by Drs Georgina Cepeda and Marina Sabatini (Consejo Nacional de Investgaciones Cientificas y Tecnicas, Argentina). Scale bar represents 0.5 mm.
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