http://lod.bco-dmo.org/id/dataset/536864
eng; USA
utf8
dataset
Highest level of data collection, from a common set of sensors or instrumentation, usually within the same research project
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
2014-10-30
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Raman spectra from several different bivalve species; analysed in the North lab at UMCES HPL from 2012-2014 (Raman Spec Bivalves project)
2014-11-10
publication
2014-11-10
revision
BCO-DMO Linked Data URI
2014-11-10
creation
http://lod.bco-dmo.org/id/dataset/536864
Elizabeth North
University of Maryland Center for Environmental Science
principalInvestigator
Dr Christine Thompson
University of Maryland Center for Environmental Science
principalInvestigator
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
publisher
Cite this dataset as: North, E., Thompson, C. (2014) Raman spectra from several different bivalve species; analysed in the North lab at UMCES HPL from 2012-2014 (Raman Spec Bivalves project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 10 November 2014) Version Date 2014-11-10 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/536864 [access date]
Raman spectra from several different bivalve species. Dataset Description: <p>This data set contains Raman spectra of the following species: <em>Argopecten irradians, Crassostrea gigas, Crassostrea virginica, Gemma gemma, Geukensia demissa, Ischadium recurvum, Macoma mitchelli, Mercenaria mercenaria, Mulinia lateralis, Mya arenaria, Mytilopsis leucophaeata, Ostrea lurida, Rangia cuneata, Tagelus plebeius, Spisula solidissma, Panopea generosa</em>. Detailed information on the source and preparation of larvae can be found in Thompson et al. (<em>in prep</em>). All spectra were acquired by Adam Schlenger and Christine Thompson.</p> Methods and Sampling: <p>Detailed information on the source and preparation of larvae can be found in Thompson et al. (<em>in prep</em>). All spectra were acquired by Adam Schlenger and Christine Thompson. The following information on the acquisition and processing of the spectra that comprise this dataset was quoted from Thompson et al. (<em>in prep</em>):</p>
<p>"Raman spectra were acquired with an XploRA confocal Raman microscope by Horiba Jobin Yvon, Inc. The system includes a flat field spectrograph with a multichannel air cooled CCD detector and color camera optically coupled to an Olympus BX41 microscope. We used three lasers: a 532 nm 25 mW solid-state laser, a 638 nm 25 mW laser diode, and a 785 nm 25 mW laser diode. The lasers ran through a 100x objective using a 1200 grove mm<sup>-1</sup> grating and hole and slit size of 300 µm and 100 µm, respectively. Spectra were recorded in the range of 200-2000 cm<sup>-1</sup>. Spectra were acquired from 20 larval shells for each sample by averaging 3 accumulations with an exposure time of 10 s. For one shell in each sample, three spectra were taken from different positions on the shell. Spectral acquisition was controlled using Horiba’s LabSpec software (version 6). Wavelength calibration was performed on the XploRA system using a neon light source that was calibrated daily with a silicon wafer.</p>
<p>All spectra were first pre-processed to remove noise and other variability. Immediately after acquisition, noise was removed using a smoothing function in LabSpec. Baseline correction was then performed using a freely-available integrated software system for processing Raman spectra (Reisner et al. 2011) implemented in MATLAB (v. R2011a). Next, all wavenumbers were shifted to ensure the aragonite peak for all spectra fell at 1085 cm<sup>-1</sup> and then spectra were standardized to the intensity of the aragonite peak on a scale of 0 to 1."</p>
<p>The two columns of numbers in each file correspond to <em>wavenumber</em> with units of cm<sup>-1</sup> (first column) and <em>relative intensity</em> which is unitless (second column).</p>
<p><strong>References:</strong><br />
Reisner, L.A., Cao, A., &amp; Pandya, A.K. 2011. An integrated software system for processing, analyzing, and classifying Raman spectra. Chemom Intell Lab Syst 105:83–90. doi: <a href="http://dx.doi.org/10.1016/j.chemolab.2010.09.011" target="_blank">10.1016/j.chemolab.2010.09.011</a></p>
<p>Thompson, C.M., North, E.W., Kennedy, V.S., &amp; White, S.N. <em>In prep</em>. Classifying bivalve larvae using shell pigments identified by Raman spectra. Analytical and Bioanalytical Chemistry.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1240266 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1240266
completed
Elizabeth North
University of Maryland Center for Environmental Science
410-221-8497
5745 Lovers Lane
Cambridge
MD
21613
USA
enorth@umces.edu
pointOfContact
Dr Christine Thompson
University of Maryland Center for Environmental Science
410-221-8337
Horn Point Laboratory
MD
USA
cthompson@umces.edu
pointOfContact
asNeeded
Dataset Version: 10 November 2014
Unknown
wavelength
species_name
species_code
year
loc_code
location
city
state
day
loc_additional
shell_num
position
file_name
wavenumber
relative_intensity
XploRA confocal Raman microscope
theme
None, User defined
wavelength_general
species scientific name (binomial)
taxon_code
year
Site_ID
site
age
No BCO-DMO term
featureType
BCO-DMO Standard Parameters
Raman Microscope
instrument
BCO-DMO Standard Instruments
lab_North_Raman_Spectra
service
Deployment Activity
Cambridge, MD
place
Locations
otherRestrictions
otherRestrictions
Access Constraints: none. Use Constraints: Please follow guidelines at: http://www.bco-dmo.org/terms-use Distribution liability: Under no circumstances shall BCO-DMO be liable for any direct, incidental, special, consequential, indirect, or punitive damages that result from the use of, or the inability to use, the materials in this data submission. If you are dissatisfied with any materials in this data submission your sole and exclusive remedy is to discontinue use.
Can Raman spectroscopy be used as a high-accuracy method to identify bivalve larvae?
https://osprey.bco-dmo.org/project/535551
Can Raman spectroscopy be used as a high-accuracy method to identify bivalve larvae?
<p>Identification of bivalve larvae is notoriously difficult and time consuming; currently no ‘gold standard’ method exists for distinguishing larvae collected in the field. We proposed to determine if Raman spectroscopy could be used to identify species of bivalve larvae. Raman spectroscopy is a non-destructive method that uses a focused laser to produce a spectrum, a graph with peaks that indicate the presence of different molecules like calcium carbonate and organic pigments. Previous work exploring the use of Raman spectroscopy on shells of bivalve larvae revealed that larval shells of the eastern oyster (<em>Crassostrea virginica</em>) exhibit a unique spectrum at one wavelength which was distinguishable from those of six other bivalve species. The objective of this research was to analyze additional species of larvae and to determine if spectra collected at three different wavelengths could be used to distinguish the larvae. We collected Raman spectra at three wavelengths from 25 samples of bivalve larvae representing 16 species and four taxonomic Orders. Use of the Raman spectra with three wavelengths enabled classification of larvae into Order/Family groups with accuracies ≥ 92% (Thompson et al. <em>in prep</em>). This study indicates that continued evaluation of this approach would be a fruitful line of research which could advance knowledge of shellfish biology and ecology.</p>
<p><em>(Project description provided by Dr. Elizabeth North.)</em></p>
Raman Spec Bivalves
largerWorkCitation
project
eng; USA
biota
oceans
Cambridge, MD
2014-11-10
0
BCO-DMO catalogue of parameters from Raman spectra from several different bivalve species; analysed in the North lab at UMCES HPL from 2012-2014 (Raman Spec Bivalves project)
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
http://lod.bco-dmo.org/id/dataset-parameter/537919.rdf
Name: wavelength
Units: nanometers (nm)
Description: <p>Wavelength of the laser light source used (532, 638, or 785).</p>
http://lod.bco-dmo.org/id/dataset-parameter/537920.rdf
Name: species_name
Units: text
Description: <p>Name of the species.</p>
http://lod.bco-dmo.org/id/dataset-parameter/537921.rdf
Name: species_code
Units: text
Description: <p>Unique species code.</p>
http://lod.bco-dmo.org/id/dataset-parameter/537922.rdf
Name: year
Units: YYYY
Description: <p>4-digit year of spawning.</p>
http://lod.bco-dmo.org/id/dataset-parameter/537923.rdf
Name: loc_code
Units: text
Description: <p>Unique sample location code.</p>
http://lod.bco-dmo.org/id/dataset-parameter/537924.rdf
Name: location
Units: text
Description: <p>Sample location.</p>
http://lod.bco-dmo.org/id/dataset-parameter/537925.rdf
Name: city
Units: text
Description: <p>City of the sample location.</p>
http://lod.bco-dmo.org/id/dataset-parameter/537926.rdf
Name: state
Units: text
Description: <p>2-letter abbreviation for the state of the sample location.</p>
http://lod.bco-dmo.org/id/dataset-parameter/537927.rdf
Name: day
Units: number of days
Description: <p>Age of larvae in days in the format DX where X = how many days old the larva was*. For specimens where age was unclear: DS = d-stage;<br />
VE = veliger;<br />
PV = pedi-veliger larvae (unclear how old);<br />
R = larvae released from brood (for brooding species);<br />
H = larvae at time of harvest (for brooding species).<br />
*For RCSL samples, day 13 is written as 13D</p>
http://lod.bco-dmo.org/id/dataset-parameter/537928.rdf
Name: loc_additional
Units: text
Description: <p>Additional location marker for some samples of Mytilopsis leucophaeata; Mulinia lateralis; and Macoma mitchelli. CT = Choptank River (Maryland USA). nd = not applicable/no additional location code.</p>
http://lod.bco-dmo.org/id/dataset-parameter/537929.rdf
Name: shell_num
Units: alphanumeric
Description: <p>Shell number in the format SXX where XX = number shell (1-20 usually).</p>
http://lod.bco-dmo.org/id/dataset-parameter/537930.rdf
Name: position
Units: alphanumeric
Description: <p>Position number in the format PX where X = position (some shells had multiple positions for spectra).</p>
http://lod.bco-dmo.org/id/dataset-parameter/537931.rdf
Name: file_name
Units: text
Description: <p>Name of the original spectra file containing the wavenumber and relative_intensity. Notes:<br />
sd = standardized to aragonite 1085 peak;<br />
pp = post-processed (flattened, noise reduction).</p>
http://lod.bco-dmo.org/id/dataset-parameter/537932.rdf
Name: wavenumber
Units: per centimeter (cm-1)
Description: <p>Wavenumber.</p>
http://lod.bco-dmo.org/id/dataset-parameter/537933.rdf
Name: relative_intensity
Units: unitless
Description: <p>Relative intensity.</p>
GB/NERC/BODC > British Oceanographic Data Centre, Natural Environment Research Council, United Kingdom
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
893358118
https://datadocs.bco-dmo.org/file/8XXgyG5tXNwGvy/raman_spectra.csv
raman_spectra.csv
Primary data file for dataset ID 536864
download
https://osprey.bco-dmo.org/dataset/536864/data/download
download
onLine
dataset
<p>Detailed information on the source and preparation of larvae can be found in Thompson et al. (<em>in prep</em>). All spectra were acquired by Adam Schlenger and Christine Thompson. The following information on the acquisition and processing of the spectra that comprise this dataset was quoted from Thompson et al. (<em>in prep</em>):</p>
<p>"Raman spectra were acquired with an XploRA confocal Raman microscope by Horiba Jobin Yvon, Inc. The system includes a flat field spectrograph with a multichannel air cooled CCD detector and color camera optically coupled to an Olympus BX41 microscope. We used three lasers: a 532 nm 25 mW solid-state laser, a 638 nm 25 mW laser diode, and a 785 nm 25 mW laser diode. The lasers ran through a 100x objective using a 1200 grove mm<sup>-1</sup> grating and hole and slit size of 300 µm and 100 µm, respectively. Spectra were recorded in the range of 200-2000 cm<sup>-1</sup>. Spectra were acquired from 20 larval shells for each sample by averaging 3 accumulations with an exposure time of 10 s. For one shell in each sample, three spectra were taken from different positions on the shell. Spectral acquisition was controlled using Horiba’s LabSpec software (version 6). Wavelength calibration was performed on the XploRA system using a neon light source that was calibrated daily with a silicon wafer.</p>
<p>All spectra were first pre-processed to remove noise and other variability. Immediately after acquisition, noise was removed using a smoothing function in LabSpec. Baseline correction was then performed using a freely-available integrated software system for processing Raman spectra (Reisner et al. 2011) implemented in MATLAB (v. R2011a). Next, all wavenumbers were shifted to ensure the aragonite peak for all spectra fell at 1085 cm<sup>-1</sup> and then spectra were standardized to the intensity of the aragonite peak on a scale of 0 to 1."</p>
<p>The two columns of numbers in each file correspond to <em>wavenumber</em> with units of cm<sup>-1</sup> (first column) and <em>relative intensity</em> which is unitless (second column).</p>
<p><strong>References:</strong><br />
Reisner, L.A., Cao, A., &amp; Pandya, A.K. 2011. An integrated software system for processing, analyzing, and classifying Raman spectra. Chemom Intell Lab Syst 105:83–90. doi: <a href="http://dx.doi.org/10.1016/j.chemolab.2010.09.011" target="_blank">10.1016/j.chemolab.2010.09.011</a></p>
<p>Thompson, C.M., North, E.W., Kennedy, V.S., &amp; White, S.N. <em>In prep</em>. Classifying bivalve larvae using shell pigments identified by Raman spectra. Analytical and Bioanalytical Chemistry.</p>
Specified by the Principal Investigator(s)
<p>BCO-DMO downloaded the original data files from the DropBox URL provided by Dr. E. North. BCO-DMO created additional data columns for serving based on the file name conventions and metadata. See the original metadata form describing the file name conventions: <a href="http://dmoserv3.whoi.edu/data_docs/Raman_Spectra/Metadata_for_Raman_Spectra_of_Bivalve_Larvae_final_29Oct14_revised.pdf">Metadata_for_Raman_Spectra_of_Bivalve_Larvae</a> (PDF file).</p>
Specified by the Principal Investigator(s)
asNeeded
7.x-1.1
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
XploRA confocal Raman microscope
XploRA confocal Raman microscope
PI Supplied Instrument Name: XploRA confocal Raman microscope PI Supplied Instrument Description:Raman spectra were acquired with an XploRA confocal Raman microscope by Horiba Jobin Yvon, Inc. The system includes a flat field spectrograph with a multichannel air cooled CCD detector and color camera optically coupled to an Olympus BX41 microscope. The investigators used three lasers: a 532 nm 25 mW solid-state laser, a 638 nm 25 mW laser diode, and a 785 nm 25 mW laser diode. See more information about the Raman microscope on the UMCES website. Instrument Name: Raman Microscope Instrument Short Name: Instrument Description: The Raman microscope is a laser-based microscopic device used to perform Raman spectroscopy. The Raman microscope begins with a standard optical microscope, and adds an excitation laser, laser rejection filters, a spectrometer or monochromator, and an optical sensitive detector such as a charge-coupled device (CCD), or photomultiplier tube, (PMT). One example is the XploRA confocal Raman microscope (information from the manufacturer).
Deployment: lab_North_Raman_Spectra
lab_North_Raman_Spectra
UMCES_HPL_labs
laboratory
lab_North_Raman_Spectra
Elizabeth North
University of Maryland Center for Environmental Science
UMCES_HPL_labs
laboratory