http://lod.bco-dmo.org/id/dataset/964206
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
2025-06-09
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Crystal orientation in subantarctic planktic foraminifera shells from EBSD analysis from collections in the sub-Antarctic south of South Africa between 1993 and 2016
2025-12-05
publication
2025-12-05
revision
Woods Hole Oceanographic Institution (WHOI BCO-DMO)
2026-02-19
publication
https://doi.org/10.26008/1912/bco-dmo.964206.1
Sandi M. Smart
University of Alabama-Tuscaloosa
principalInvestigator
Sarah E. Fawcett
University of Cape Town
principalInvestigator
Alberto Pérez-Huerta
University of Alabama-Tuscaloosa
principalInvestigator
Harold Stowell
University of Alabama-Tuscaloosa
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: Smart, S. M., Fawcett, S. E., Stowell, H., Pérez-Huerta, A. (2026) Crystal orientation in subantarctic planktic foraminifera shells from EBSD analysis from collections in the sub-Antarctic south of South Africa between 1993 and 2016. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2025-12-05 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.964206.1 [access date]
Dataset Description: <p>SEM = Scanning Electron Microscopy<br />
EBSD =&nbsp;Electron Backscatter Diffraction<br />
CTF = Channel Text File<br />
<br />
These data support the results publication Smart et al. (in review):<br />
Smart, S.M., S. E. Fawcett, H. Stowell &amp; A. Pérez-Huerta. (n.d.) Changes in Shell and Crystal Structure from Life to Sediments: an EBSD Characterization of Subantarctic Planktic Foraminifera. Geochemistry, Geophysics, Geosystems.&nbsp; In review.<br />
<br />
Additional funding description:<br />
In addition to NSF award OCE-2205603, this dataset was supported by South African National Research Foundation (Grants 111090 and 120714); University of Cape Town's URC Postdoctoral Fellowship.</p> Methods and Sampling: <p>Living specimens were collected using a plankton net towed at 40-60 m depth, and preserved in a pH-buffered, 5–10% formalin-seawater solution kept at 4°C. Foraminifera shells were separated using a combination of wet-sieving, NaCl density separation and dry picking under a microscope. For more details, see Smart et al. (2020). Core-top specimens were picked from the 0-1 cm sediment interval after sieving and rinsing with tap water. Most living and subfossil specimens were sonicated in high-purity ethanol, oxidatively cleaned and rinsed in MilliQ before epoxy mounting. Others were left uncleaned. Cleaning treatment is indicated in dataset file "foram_ebsd_supplemental_metadata.csv" and Supplemental Table S1&nbsp;of the companion publication to this dataset (Smart et al., in review). Once fully dry, shells were mounted in EpoThin 2 epoxy, cured, and cross-sectioned using SiC grit-papers and Alumina polish with progressively smaller particle sizes. Shortly before EBSD analysis, sample mounts were coated with ~4-5 nm gold. For details, see Smart et al. (in review).</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-2205603 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=2205603
completed
Sandi M. Smart
University of Alabama-Tuscaloosa
sandi.smart@alumni.uct.ac.za
pointOfContact
Sarah E. Fawcett
University of Cape Town
021 650 5369
Department of Oceanography 134 R.W. James Building
sarah.fawcett@uct.ac.za
pointOfContact
Alberto Pérez-Huerta
University of Alabama-Tuscaloosa
aphuerta@ua.edu
pointOfContact
Harold Stowell
University of Alabama-Tuscaloosa
hstowell@ua.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
Folder_name
File_name
Site
cruise_id
lat
lon
DateTime_Start_GMT
DateTime_End_GMT
depth
Species
Specimen
Type
Chamber
Phase
X
Y
Bands
Error
Euler1
Euler2
Euler3
MAD
BC
BS
Xcells
Ycells
XStep
YStep
JEOL 7000 field emission scanning electron microscope (FE-SEM)
theme
None, User defined
sample description
file_name
tow
Cruise identfier
latitude
longitude
ISO_DateTime_UTC
depth
taxon_code
sample type
No BCO-DMO term
quality flag
Pixel size in X direction
Pixel size in the Y direction
featureType
BCO-DMO Standard Parameters
Scanning Electron Microscope
instrument
BCO-DMO Standard Instruments
VOY016
VOY019
ANT-XI/2
service
Deployment Activity
Amundsen Sea; Bellingshausen Sea; Bransfield Strait; Marguerite Bay; South Pacific Ocean
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.
OCE-PRF: A submicron scale investigation of foraminifera-bound organic matter: implications for preservation and the paleo-δ15N proxy
https://osprey.bco-dmo.org/project/957025
OCE-PRF: A submicron scale investigation of foraminifera-bound organic matter: implications for preservation and the paleo-δ15N proxy
<p>NSF abstract:<br />
This project dives into the microscopic world of planktic foraminifera, tiny shelled zooplankton that inhabit oceans across the globe. As foraminifera build their shells, they incorporate tiny amounts or organic matter and, with it, information about their surroundings and ecology. When their shells sink and gather on the seafloor, they add to an ever-growing archive of Earth history. Exactly how well the organic matter and its original signals are preserved in shells during sinking and early burial is a key uncertainty for its use in reconstructing past climate. To address this, the PI will use ultra-high resolution crystal and chemical mapping to compare shells before and after this crucial transition to the fossil record. Understanding the feedbacks that have regulated Earth’s climate in the past is an essential part of our future response and preparedness as a nation to face the challenges of a warming planet, and is thus well aligned with NSF directives. Furthermore, by characterizing the biomineral structures of modern shells, this work will assist with monitoring ocean acidification, which can compromise fisheries, tourism and the natural buffering of coastal communities from storms (e.g., by coral reefs). As a female scientist and immigrant from a developing country, the PI is dedicated to encouraging other young women and underrepresented groups to pursue a career in science. By partnering with a local Alabama middle school that serves underrepresented students, she hopes to inspire those who might not otherwise consider science as a career path, to take STEM subjects in high school. In this way, students will be better equipped to take on the challenge of climate change, and be made aware of the need for their talents in building a more sustainable future. The nitrogen (N) isotope composition (δ15N) of organic matter within the shell walls of planktic foraminifera is emerging as a promising new tool for tracking the amount and partitioning of nitrogen, an essential nutrient for life, in the ocean. The number of foraminifera-bound δ15N records has grown rapidly in recent years, yielding tantalizing insights into the interplay between ocean fertility, oxygen concentrations and atmospheric greenhouse gas levels. Yet, fundamental questions remain about the mechanism of N incorporation into calcite, taxonomic differences in N uptake, and the preservation potential of the organic matter to which N is bound, particularly in the earliest stages of sinking and burial. The utility of bulk geochemical analyses (which require combining hundreds of shells) in answering these questions is limited by inherent issues of scale. Hence, the PI proposes to use electron backscatter diffraction (EBSD) and nanoscale secondary ion mass spectrometry (NanoSIMS) on individual shells from living (tow-caught) and dead (seafloor sediment) assemblages to evaluate changes in the biomineral structure, organic matter distribution and relative N content of foraminifera shells from life in the surface ocean to burial on the seafloor. The PI expects her investigation will also provide insight into the role of organic matter in the formation (i.e., biomineralization) and behavior (e.g., susceptibility to breakage/dissolution, mineral-fluid exchange) of biogenic calcite, a geologically important material of interest to a broad range of scientists. Thus while her specific motivation for this work is the N isotope paleo-proxy, the implications extend beyond N to other systems of organic matter and associated tracers (e.g., δ34S, I/Ca, Na/Ca), and to fundamental research areas like habitability and the co-evolution of life and planet. Already, the paleo-δ15N proxy is yielding high-impact results concerning the often-complex feedbacks between the marine biosphere and climate. Thus, by seeking to inform these interpretations, the proposed work has the potential to help predict the unintended consequences of a rapidly warming and acidifying ocean. This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.</p>
Forams at submicron scale
largerWorkCitation
project
eng; USA
oceans
Amundsen Sea; Bellingshausen Sea; Bransfield Strait; Marguerite Bay; South Pacific Ocean
8.736683
26.831
-42.883
-40.958833
1993-12-01
2024-05-31
Sub-Antarctic ocean and sediments
0
BCO-DMO catalogue of parameters from Crystal orientation in subantarctic planktic foraminifera shells from EBSD analysis from collections in the sub-Antarctic south of South Africa between 1993 and 2016
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/983740.rdf
Name: Folder_name
Units: unitless
Description: <p>Folder name within zip packages containing the .ctf files: EBSDdatafiles_corr.zip</p>
http://lod.bco-dmo.org/id/dataset-parameter/983741.rdf
Name: File_name
Units: unitless
Description: <p>name of the corresponding .ctf (EBSD) file within EBSDdatafiles_corr.zip</p>
http://lod.bco-dmo.org/id/dataset-parameter/983742.rdf
Name: Site
Units: unitless
Description: <p>tow name (W1, W2 or M10 from Smart et al., 2020) or core-top site name (PS2489-4)</p>
http://lod.bco-dmo.org/id/dataset-parameter/983771.rdf
Name: cruise_id
Units: unitless
Description: <p>Cruise identifier</p>
http://lod.bco-dmo.org/id/dataset-parameter/983743.rdf
Name: lat
Units: decimal degrees
Description: <p>Latitude</p>
http://lod.bco-dmo.org/id/dataset-parameter/983744.rdf
Name: lon
Units: decimal degrees
Description: <p>Longitude</p>
http://lod.bco-dmo.org/id/dataset-parameter/983745.rdf
Name: DateTime_Start_GMT
Units: unitless
Description: <p>Start DateTime with Timezone (ISO 8601 format)</p>
http://lod.bco-dmo.org/id/dataset-parameter/983746.rdf
Name: DateTime_End_GMT
Units: unitless
Description: <p>End DateTime with Timezone (ISO 8601 format)</p>
http://lod.bco-dmo.org/id/dataset-parameter/983747.rdf
Name: depth
Units: meters (m)
Description: <p>Depth</p>
http://lod.bco-dmo.org/id/dataset-parameter/983748.rdf
Name: Species
Units: unitless
Description: <p>Species code. inf = Globorotalia inflata; tru = Globorotalia truncatulinoides.</p>
http://lod.bco-dmo.org/id/dataset-parameter/983749.rdf
Name: Specimen
Units: unitless
Description: <p>Shorthand identifier for individual shell</p>
http://lod.bco-dmo.org/id/dataset-parameter/983750.rdf
Name: Type
Units: unitless
Description: <p>Sample type. tow = live-collected via net-tow; ctop = core-top (subfossil) from surface sediments</p>
http://lod.bco-dmo.org/id/dataset-parameter/983751.rdf
Name: Chamber
Units: unitless
Description: <p>Chamber identifier. F0 is the most recently formed (normally the largest) chamber of the shell. </p>
http://lod.bco-dmo.org/id/dataset-parameter/983752.rdf
Name: Phase
Units: unitless
Description: <p>Phase. Whether pixel was indexed as calcite. no units; 1 = calcite, 0 = non-indexed</p>
http://lod.bco-dmo.org/id/dataset-parameter/983753.rdf
Name: X
Units: micrometers (um)
Description: <p>The position of pixel in the x-direction (right/east = positive)</p>
http://lod.bco-dmo.org/id/dataset-parameter/983754.rdf
Name: Y
Units: micrometers (um)
Description: <p>The position of pixel in the y-direction (top/north = positive)</p>
http://lod.bco-dmo.org/id/dataset-parameter/983755.rdf
Name: Bands
Units: unitless
Description: <p>The number of Kikuchi bands detected and used for indexing</p>
http://lod.bco-dmo.org/id/dataset-parameter/983756.rdf
Name: Error
Units: unitless
Description: <p>error flag. error = 0 means no flag; error = 3 appears to be non-indexed (i.e., no solution for that pixel)</p>
http://lod.bco-dmo.org/id/dataset-parameter/983757.rdf
Name: Euler1
Units: degrees
Description: <p>First euler angle, φ1 (phi1). Rotation around z axis. Euler angles for a specific EBSD datapoint are the minimum rotations around the X-Y-Z axes needed for the map reference frame to match that pixel's crystallographic reference frame.</p>
http://lod.bco-dmo.org/id/dataset-parameter/983758.rdf
Name: Euler2
Units: degrees
Description: <p>Second euler angle, Φ (phi). Rotation around x axis. Euler angles for a specific EBSD datapoint are the minimum rotations around the X-Y-Z axes needed for the map reference frame to match that pixel's crystallographic reference frame.</p>
http://lod.bco-dmo.org/id/dataset-parameter/983759.rdf
Name: Euler3
Units: degrees
Description: <p>Third euler angle, φ2 (phi2). Rotation around new z axis). Euler angles for a specific EBSD datapoint are the minimum rotations around the X-Y-Z axes needed for the map reference frame to match that pixel's crystallographic reference frame.</p>
http://lod.bco-dmo.org/id/dataset-parameter/983760.rdf
Name: MAD
Units: degrees
Description: <p>Mean Angular Deviation (MAD) misfit between measured and calculated angles between Kikuchi bands. Indicator of confidence in indexing</p>
http://lod.bco-dmo.org/id/dataset-parameter/983761.rdf
Name: BC
Units: unitless
Description: <p>Band Contrast (BC); a measure of diffraction signal intensity. Indicator of pattern quality. no units (relative measure)</p>
http://lod.bco-dmo.org/id/dataset-parameter/983762.rdf
Name: BS
Units: unitless
Description: <p>Band Slope (BS); a measure of Kikuchi band edge sharpness. Indicator of pattern quality and indexing confidence. no units (relative measure)</p>
http://lod.bco-dmo.org/id/dataset-parameter/983763.rdf
Name: Xcells
Units: unitless
Description: <p>number of pixels in the X direction</p>
http://lod.bco-dmo.org/id/dataset-parameter/983764.rdf
Name: Ycells
Units: unitless
Description: <p>number of pixels in the Y direction</p>
http://lod.bco-dmo.org/id/dataset-parameter/983765.rdf
Name: XStep
Units: micrometers (um)
Description: <p>step size in the X direction</p>
http://lod.bco-dmo.org/id/dataset-parameter/983766.rdf
Name: YStep
Units: micrometers (um)
Description: <p>step size in the Y direction</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
https://doi.org/10.26008/1912/bco-dmo.964206.1
download
onLine
dataset
<p>Living specimens were collected using a plankton net towed at 40-60 m depth, and preserved in a pH-buffered, 5–10% formalin-seawater solution kept at 4°C. Foraminifera shells were separated using a combination of wet-sieving, NaCl density separation and dry picking under a microscope. For more details, see Smart et al. (2020). Core-top specimens were picked from the 0-1 cm sediment interval after sieving and rinsing with tap water. Most living and subfossil specimens were sonicated in high-purity ethanol, oxidatively cleaned and rinsed in MilliQ before epoxy mounting. Others were left uncleaned. Cleaning treatment is indicated in dataset file "foram_ebsd_supplemental_metadata.csv" and Supplemental Table S1&nbsp;of the companion publication to this dataset (Smart et al., in review). Once fully dry, shells were mounted in EpoThin 2 epoxy, cured, and cross-sectioned using SiC grit-papers and Alumina polish with progressively smaller particle sizes. Shortly before EBSD analysis, sample mounts were coated with ~4-5 nm gold. For details, see Smart et al. (in review).</p>
Specified by the Principal Investigator(s)
<p>Here we provide the original AZtec crystal orientation files (in .ctf format) as well as the corrected and minimally processed data (as both .ctf files and .txt files). During data collection, the software automatically compares the collected EBSD patterns with calcite in the American Mineralogist crystal structure database to find the best fit (i.e., crystal orientation). Data files in .ctf format can be loaded into any standard EBSD software (e.g., EDAX OIM Analysis; https://www.edax.com/products/ebsd/oim-analysis) or using the&nbsp;free, open-source MTEX toolbox using MATLAB (https://mtex-toolbox.github.io/) as done in Smart et al. (2026,&nbsp;<em>in press</em>). &nbsp;See Hiscocks, J. (2021) "Getting Started with MTEX for EBSD analysis Rev6" for further guidance on loading .ctf files.</p>
<p>Our data correction and processing steps include:</p>
<p>1) Applying a 180° rotation to the Z axis (i.e., around the sample normal) to correct for a difference in reference frame between the data collection software (AZtec) and the analysis software we used (MTEX). This is the same correction we use for our own analysis in Smart et al. (in review).</p>
<p>2) Converting from the spatial reference frame to the Euler reference frame. This step aligns the map axes with the crystal axes (i.e., the Euler rotation axes) so that the X axis of the map corresponds to the X axis of rotation in the Euler angle system. Euler angles for a specific EBSD data-point are the minimum rotations around the X-Y-Z axes needed for the map frame to match that pixel's crystallographic frame.</p>
<p>3) Basic quality control: We removed any data with a mean angular deviation (MAD) &gt;2.5° as well as any grains smaller than 2 pixels with MAD&gt;1°. Note that we define a grain (domain of similar orientation) using a threshold of 5°. Areas containing epoxy (i.e., not within the calcite shell) were also excluded. We did not apply any algorithms for de-noising, smoothing or indexing of non-indexed pixels.&nbsp;</p>
<p>We also provide supplemental metadata (foram_ebsd_supplemental_metadata.csv), which contains additional&nbsp;metadata for each .ctf map file (species, collection type, site, chamber mapped), and summary statistics on crystal orientation observed in our specimens (e.g., abundance of different crystal twinning relationships).</p>
Specified by the Principal Investigator(s)
Data Files:
EBSDdatafiles_corr.zip = Contains the corrected .Channel Text Files (.ctf) crystal orientation data files.
* Each corrected .ctf file was concatenated into one table and imported into the BCO-DMO data system. The combined table appears as Data File: 964206_v1_foram_ebsd_crystal_orientation.csv (along with other download format options).
* Experiment and collection metadata (Specimen, Type, Species, Chamber, Site, lat, lon, depth,cruise_id,DateTime_Start_GMT,DateTime_End_GMT) was added to the combined table (joined on corrected ctf filename) from supplemental file foram_ebsd_supplemental_metadata.csv
* Missing Data Identifiers:
In the BCO-DMO data system missing data identifiers are displayed according to the format of data you access. For example, in csv files it will be blank (null) values. In Matlab .mat files it will be NaN values. When viewing data online at BCO-DMO, the missing value will be shown as blank (null) values.
* Column names adjusted to conform to BCO-DMO naming conventions designed to support broad re-use by a variety of research tools and scripting languages. [Only numbers, letters, and underscores. Can not start with a number]
* Lat and Lon in the combined table was rounded to five decimal places.
---
Supplemental files:
EBSDdatafiles_orig.zip = All the original (uncorrected) crystal orientation .ctf files were packaged into this zip file. See more information in the file description and Data Processing sections.
EBSDdatafiles_corr_txt.zip = All the corrected .txt data files were packaged into this zip file. Same data as the corrected .ctf data files, files differ in formatting. See more information in the file description and Data Processing sections.
foram_ebsd_supplemental_metadata.csv
* A table corresponding to Table S1 in the pending publication Smart et al. (2026, in press) TableS1_Summary-statistics.xlsx was revised and resubmitted to BCO-DMO with additional collection metadata, including date,start and end times, depth, lat, lon etc. The revised file "foram_ebsd_supplemental_metadata_update20251203.csv" was imported into the BCO-DMO data system, columns for datetime with timezone were added, and file column names were adjusted to match BCO-DMO naming conventions. The attached to this dataset as supplemental file foram_ebsd_supplemental_metadata.csv.
* negative (-) prefixed to latitude values to indicate degrees South (format: Decimal Degrees where South and West are negative). The location of this dataset is Sub-Antarctic south of South Africa.
* Column Data Filename updated to be "Orig_Filename" (corresponding to file within EBSDdatafiles_orig.zip) and a second column "Corrected_Filename" (corresponding to the file within EBSDdatafiles_corr.zip)
Specified by BCO-DMO Data Managers
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
JEOL 7000 field emission scanning electron microscope (FE-SEM)
JEOL 7000 field emission scanning electron microscope (FE-SEM)
PI Supplied Instrument Name: JEOL 7000 field emission scanning electron microscope (FE-SEM) PI Supplied Instrument Description:SEM-EBSD analysis was performed using a JEOL 7000 field emission scanning electron microscope (FE-SEM) fitted with an Oxford Instruments HKL Nordlys EBSD detector. Beam settings were 15-25 kV and 12-20 nA at X1000-3000 magnification, yielding an average step-size of 0.15 μm for our maps. Instrument Name: Scanning Electron Microscope Instrument Short Name:SEM Instrument Description: A scanning electron microscope (SEM) scans a focused electron beam over a surface to create an image. The electrons in the beam interact with the sample, producing various signals that can be used to obtain information about the surface topography and composition.
Cruise: VOY016
VOY016
Community Standard Description
International Council for the Exploration of the Sea
R/V S.A. Agulhas II
vessel
VOY016
Sandy Thomalla
Council for Scientific and Industrial Research
Cruise: VOY019
VOY019
Community Standard Description
International Council for the Exploration of the Sea
R/V S.A. Agulhas II
vessel
VOY019
Hans M. Verheye
South African Department of Environmental Affairs
Cruise: ANT-XI/2
ANT-XI/2
Community Standard Description
International Council for the Exploration of the Sea
R/V Polarstern
vessel
ANT-XI/2
Dr Rainer Gersonde
Alfred Wegener Institute for Polar and Marine Research
https://doi.org/10.2312/BzP_0188_1996
Report describing ANT-XI/2
Community Standard Description
International Council for the Exploration of the Sea
R/V S.A. Agulhas II
vessel