http://lod.bco-dmo.org/id/dataset/932252
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
2024-07-11
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
ZooProcess and Ecotaxa output from ZooSCANs of zooplankton collected along physical gradients during OAPS MOCNESS tows during R/V Oceanus northwest Atlantic 2011 cruise OC473 and R/V New Horizon northeast Pacific 2012 cruise NH1208 and imaged in 2021-2022
2024-07-11
publication
2024-07-11
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2024-10-07
publication
https://doi.org/10.26008/1912/bco-dmo.932252.1
Leocadio Blanco-Bercial
Bermuda Institute of Ocean Sciences
principalInvestigator
Amy Maas
Bermuda Institute of Ocean Sciences
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: Blanco-Bercial, L., Maas, A., Gossner, H. (2024) ZooProcess and Ecotaxa output from ZooSCANs of zooplankton collected along physical gradients during OAPS MOCNESS tows during R/V Oceanus northwest Atlantic 2011 cruise OC473 and R/V New Horizon northeast Pacific 2012 cruise NH1208 and imaged in 2021-2022. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2024-07-11 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.932252.1 [access date]
Dataset Description: <p>Acknowledgment:</p>
<p>This dataset utilized samples and data funded by a previous NSF award (OCE-1041068) "Horizontal and Vertical Distribution of Thecosome Pteropods in Relation to Carbonate Chemistry in the Northwest Atlantic and Northeast Pacific (OAPS)" https://www.bco-dmo.org/project/2154.</p> Methods and Sampling: <div>
<p><strong>Location:&nbsp;</strong></p>
<p>Northwestern Atlantic, 0 to 1000m depth, 35N, 52W to 50N, 42W along CLIVAR/WOCE line A20<br />
Northeastern Pacific, 0 to 1000m depth, 50N, 150W to 35N, 135W along CLIVAR/WOCE line P17N<br />
<br />
<strong>Methodology:&nbsp;</strong></p>
<p>To obtain samples, a 1m<sup>2</sup>&nbsp;Multiple Opening/Closing Net and Environmental Sensing System &nbsp;(MOCNESS; Wiebe et al., 1985) equipped with nine 150 m nets was deployed during the mid-day and mid-night on cruises carried out as described in &nbsp;<a href="https://www.bco-dmo.org/dataset/3546" style="box-sizing: inherit; color: rgb(0, 102, 153); cursor: pointer; text-decoration-line: none; vertical-align: baseline; margin: 0px; padding: 0px; border: 0px; font: inherit;"><u>https://www.bco-dmo.org/dataset/3546</u></a>. Briefly, sampling was at consistent intervals including 1000-800, 800-600, 600-400, 400-200, 200-100, 100-50, 50-25, 25-0m at day/night stations from 35 to 50 N in the northwest Atlantic in 2011, and from 35 and 50N along CLIVAR line P17N &nbsp;in 2012.</p>
<p>Upon retrieval, the catch from each of the eight discrete nets were divided into splits. One-half of a sample was preserved in 95% ethanol, one quarter was preserved in 5% buffered formalin, and one quarter was used for live viewing and picking, and then preserved in 70% ethanol.</p>
<p>A representative subsample of the formalin-preserved zooplankton community from each net were imaged using a ZooSCAN ver. 4 at&nbsp; either 4,800 dpi with a narrow frame, or 2400 dpi with a large frame (following the methods in: Gorsky et al., 2010, Vandromme et al., 2012, as detailed in Maas et al. 2021). Scanning resolution was changed partway through the project in accordance with advice from Hydroptic (written communication). In order to better represent all size classes in the images, the original sample was divided into three size categories. All individuals larger than 2 cm were selected by eye and scanned separately from all the others ("d1"). The remainder of the sample was sieved through a 1-mm mesh sieve, and both size fractions ("d2" &gt;1000um but excluding d1; "d3" between 150-1000um) were individually scanned. From these smaller size fractions, at least 1500 particles were scanned after subsampling using a Motoda splitter (Motoda, 1959), requiring generation of two separate scans for both size classes. This resulted in a total of five images per net.</p>
</div>
<div>
<p><strong>ZooSCAN&nbsp;Image names:</strong><br />
<br />
<span style="font-size:13px">Image names&nbsp;include:&nbsp;</span>cruise#_mocnessID_net#_sizefraction_ and _a|b if a replicate and end in _1.tif<br />
<br />
<span style="font-size:13px">Multiple images of the same size fraction were sometimes taken to obtain a sufficient number of particles. These replicates are named a or b. If there is no replicate they don’t have a letter in the image name. An a and b scan were always done for size classes d2 and d3.&nbsp; This was important because the split size is for the sum of a+b (e.g. if a is ¼ and b is ¼, the acq_sub_part will be 0.5).<br />
<br />
<strong>Example of ZooSCAN image names:</strong></span></p>
<p><span style="font-size:13px">ae1830_m13_n4_d3_a_1.tif&nbsp; [a replicate]<br />
ae1830_m13_n4_d3_b_1.tif&nbsp;&nbsp;</span>[a replicate]<br />
<span style="font-size:13px">ae1830_m13_n5_d1_1.tif&nbsp; &nbsp; &nbsp; </span>[no&nbsp;replicate]<br />
<br />
The "object_id" in this dataset (the particle identifier)&nbsp; is constructed the same way as the ZooSCAN image name except it as an additional _#&nbsp;at the end.&nbsp; This additional number in the object_id is added by the ZooProcess software (Hydroptic, 2016).<br />
e.g.<br />
object_id:&nbsp; &nbsp; &nbsp; &nbsp;ae1614_m3_n1_d2_a_1<strong>_100</strong><br />
image_name: ae1614_m3_n1_d2_a_1.tif</p>
<p><strong>Particle names:</strong></p>
<p>Names for particles (objects) follow the pattern "CruiseID_MocnessID_NetNumber_ScanFraction" followed by "_1_XXX", with "1" being automatically added by the software to indicate no duplicates of that scan and "XXX" being the unique particle number within that scan.&nbsp;<br />
<br />
<strong>Parameter (column name) nomenclature and data origin:&nbsp;<br />
* </strong>(see&nbsp;the "Parameters" section which contains all column information for the ecotaxa output table)</p>
<p>Parameters (column names)&nbsp;beginning with "object" include basic identifying metadata input by the user as well as all particle measurement data generated by ZooProcess. Any parameters beginning with "object_annotation" parameters are added by Ecotaxa. Parameters that begin with "sample" are sampling metadata input by the user during the scanning process.&nbsp; "Process" parameters describe the software and assumptions or corrections input during the data processing. "Acq" describes the portion of the sample scanned (input by user) and provides some summary data about the scanned image.&nbsp;</p>
<p><strong>Interpreting acq_sub_part</strong></p>
<p>The acq_sub_part is the denominator of the fraction of the sample scanned (e.g. "8" would be 1/8 or 0.125). For this project, the acq sub part is the fraction of the&nbsp;<u>whole size fraction</u>. "A" and "B" scans of the same fraction are considered to be halves of the whole fraction and can be statistically lumped together (e.g. if d2_a and d2_b from the same net were each 0.25 ("4") of that size fraction, the acq sub part will be 0.5 ("2").&nbsp;<br />
<br />
<span style="font-size:14px"><strong>Instruments summaries:</strong></span></p>
<p><strong>MOCNESS</strong></p>
<p>The Multiple Opening/Closing Net and Environmental Sensing System or MOCNESS is a family of net systems based on the Tucker Trawl principle. There are currently 8 different sizes of MOCNESS in existence which are designed for capture of different size ranges of zooplankton and micro-nekton. Each system is designated according to the size of the net mouth opening and in two cases, the number of nets it carries. The original MOCNESS (Wiebe et al, 1976) was a redesigned and improved version of a system described by Frost and McCrone (1974)(from MOCNESS manual). These nets allow for the discrete sampling of zooplankton at targeted depths while simultaneously capturing data on physical parameters. The MOCNESS used in all sampling for both cruises was a 1m<sup>2</sup>&nbsp;(mouth size) rigged as below.&nbsp;</p>
<p><strong>From OC473 Cruise Report </strong>(Lawson, et al. (2011),&nbsp;http://hdl.handle.net/1834/43091):</p>
<p>"The MOCNESS was equipped with eight 150-um mesh nets (nets 1-8; borrowed from URI) and one 333-um mesh net (net 0). The underwater unit used was #169. In addition to the standard temperature and conductivity probes the system also had a beta-type strobe-light unit for reducing avoidance of the nets by some zooplankton and possibly small fish.&nbsp; The strobe system has two units each with 12 LED sets (LUXEON Rebel LED) with peak output between 490-520 nm. Seven of the 24 LED sets were no longer working at the start of the sampling. The LEDs are powered by the MOCNESS battery and their pulse width, amplitude, flash rate period, and on/off are controlled by the MOCNESS software. For this cruise the pulse width was 2 ms, the relative amplitude was 99%, and the flash interval was 100 ms."</p>
<p><strong>From NH1208 Cruise Report</strong> (Lawson, et al. (2012), http://hdl.handle.net/1834/43090):</p>
<p>"The MOCNESS was equipped with eight 150-um mesh nets (nets 1-8; borrowed from URI) and one 333-um mesh net (net 0). The system was equipped with the standard SeaBird&nbsp; temperature and conductivity probes (units #535 and #120 respectively). The underwater unit used was #169. In addition to the standard temperature and conductivity probes the system also had a beta-type strobe-light unit for reducing avoidance of the nets by some zooplankton and possibly small fish.&nbsp; The strobe system has two units each with 12 LED sets (LUXEON Rebel LED) with peak output between 490-520 nm. Seven of the 24 LED sets were no longer working at the start of the sampling. The LEDs are powered by the MOCNESS battery and their pulse width, amplitude, flash rate period, and on/off are controlled by the MOCNESS software. For this cruise the pulse width was 2 ms, the relative amplitude was 99%, and the flash interval was 100 ms. The strobe unit was only used for the first four tows, after which problems with blowing the underwater unit 5A fuse (a symptom typical of strobe unit problems from the past) led us to disconnect it and not use it for the remainder of the tows."</p>
<p><strong>ZOOSCAN</strong></p>
<p>The ZooSCAN (CNRS patent) system makes use of scanner technology with custom lighting and a watertight scanning chamber into which liquid zooplankton samples can be placed. The scanner recovers a high-resolution, digital image and the sample can be recovered without damage.&nbsp; These digital images can then be investigated by computer processing. While the resolution of the digitized zooplankton images is lower than the image obtained using a binocular microscope, this technique has proven to be more than adequate for large sample sets. Identification of species is done by automatic comparison of the image (vignette) of each individual animal in the scanned image with a library data set which may be built by the investigator for each individual survey or imported from a previous survey. The latest machine learning algorithm allows high recognition levels even if we recommend complementary manual sorting to achieve a high number of taxonomic groups.&nbsp;Scans for this dataset performed with a ZooSCAN&nbsp;(Hydroptic, HYDROPTIC_V4) running with Vuescan (version 9.5.24) and ZooProcess (version 8.22, ImageJ macro suite). Images were taken at either 4800dpi with a narrow frame or 2400dpi with a large frame.&nbsp;</p>
</div>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1948162 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1948162
completed
Leocadio Blanco-Bercial
Bermuda Institute of Ocean Sciences
leocadio@asu.edu
pointOfContact
Amy Maas
Bermuda Institute of Ocean Sciences
508-289-2462
17 Biological Station Ferry Reach
St.George's GE 01
Bermuda
amy.maas@asu.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
object_id
object_lat_start
object_lon_start
object_date
object_time
object_ISO_DateTime_UTC
object_link
object_depth_min
object_depth_max
object_lat_end
object_lon_end
object_area
object_mean
object_stddev
object_mode
object_min
object_max
object_x
object_y
object_xm
object_ym
object_perim
object_bx
object_by
object_width
object_height
object_major
object_minor
object_angle
object_circ
object_feret
object_intden
object_median
object_skew
object_kurt
object_perc_area
object_xstart
object_ystart
object_area_exc
object_fractal
object_skelarea
object_slope
object_histcum1
object_histcum2
object_histcum3
object_xmg5
object_ymg5
object_nb1
object_nb2
object_nb3
object_compentropy
object_compmean
object_compslope
object_compm1
object_compm2
object_compm3
object_symetrieh
object_symetriev
object_symetriehc
object_symetrievc
object_convperim
object_convarea
object_fcons
object_thickr
object_tag
object_esd
object_elongation
object_range
object_meanpos
object_centroids
object_cv
object_sr
object_perimareaexc
object_feretareaexc
object_perimferet
object_perimmajor
object_circex
object_cdexc
sample_id
sample_dataportal_descriptor
sample_scan_operator
sample_ship
sample_program
sample_stationid
sample_bottomdepth
sample_ctdrosettefilename
sample_other_ref
sample_tow_nb
sample_tow_type
sample_net_type
sample_net_mesh
sample_net_surf
sample_zmax
sample_zmin
sample_tot_vol
sample_comment
sample_tot_vol_qc
sample_depth_qc
sample_sample_qc
sample_barcode
sample_duration
sample_ship_speed
sample_cable_length
sample_cable_angle
sample_cable_speed
sample_nb_jar
sample_open
process_id
process_date
process_time
process_img_software_version
process_img_resolution
process_img_od_grey
process_img_od_std
process_img_background_img
process_particle_version
process_particle_threshold
process_particle_pixel_size_mm
process_particle_min_size_mm
process_particle_max_size_mm
process_particle_sep_mask
process_particle_bw_ratio
process_software
acq_id
acq_instrument
acq_min_mesh
acq_max_mesh
acq_sub_part
acq_sub_method
acq_hardware
acq_software
acq_author
acq_imgtype
acq_scan_date
acq_scan_time
acq_quality
acq_bitpixel
acq_greyfrom
acq_scan_resolution
acq_rotation
acq_miror
acq_xsize
acq_ysize
acq_xoffset
acq_yoffset
acq_lut_color_balance
acq_lut_filter
acq_lut_min
acq_lut_max
acq_lut_odrange
acq_lut_ratio
acq_lut_16b_median
1m MOCNESS
ZooSCAN ver. 4
theme
None, User defined
individual
latitude
longitude
date_local
time_local
ISO_DateTime_UTC
external_link
depth nominal
surface_area
No BCO-DMO term
Maximum grey level (highest pixel intensity)
Pixel size in X direction
Pixel size in the Y direction
image_analysis
X coordinate of the center of the upper left pixel
y-coordinate of the center of the upper left pixel
width
height
feret diameter (Max caliper diameter)
ESD (Equivalent spherical diameter)
sample identification
sample description
person name
ship
project
station
depth
file_name
comments
site description
sample type
net mesh size
volume of water filtered
quality flag
time_elapsed
speed
instrument
instrument model
flag
featureType
BCO-DMO Standard Parameters
MOCNESS1
ZooSCAN
instrument
BCO-DMO Standard Instruments
OC473
NH1208
service
Deployment Activity
western North Atlantic, 35-50 degrees North
transect between 35 and 50N along CLIVAR line P17N
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.
Quantifying the drivers of midwater zooplankton community structure
https://www.nsf.gov/awardsearch/showAward?AWD_ID=1948162
Quantifying the drivers of midwater zooplankton community structure
<p>NSF Award Abstract: </p>
<p>Processes in the midwater region below 200 m depth, also known as the twilight zone, represent a major unknown for the biology and chemistry of the ocean. Studies of animals drifting in the oceans, known as zooplankton, are scarce due to the difficulty and associated time and costs of sampling deep waters. The advent of automated image analysis and genetic tools is leading to a rapid increase in our knowledge of the diversity, abundances and size distribution of communities in shallow waters. However, our understanding of the deeper layers of the ocean is still in its infancy, and there are few studies that combine these three facets of the ecology of the zooplankton. The objective of this project is to leverage existing samples, obtained from previously NSF-funded research in the North Pacific and North Atlantic, to study how the abundances, diversity, and size distribution of zooplankton in the midwater vary with latitude and environmental factors. Automated image analyses provide information on abundance and size, and genetic analyses give unprecedented data on the diversity of the midwater community for the North Atlantic and the North Pacific, from subtropical to subarctic environments. This project provides high quality hands-on training opportunities for at least two undergraduate researchers and generates material for undergraduate and graduate courses. Two workshops train educators on the classroom use of the NSF-funded Biological and Chemical Oceanography Data Management Office (BCO-DMO) open access oceanographic data.</p>
<p>Recent advances in image analysis and metabarcoding of zooplankton communities via new data tools are an opportunity to generate quantitative and predictive relationships between environmental drivers and zooplankton diversity, abundances and size distribution. While this information is available for plankton in epipelagic regions, the focus of this study is on midwater communities, which remain poorly characterized. Obtaining these data is the first step towards a quantitative analysis that assesses the impact of the midwater community on biogeochemical cycles. The project uses archived samples from two cruises conducted in the N. Atlantic and N. Pacific to test hypotheses about how temperature, midwater hypoxia, primary productivity and biogeographic province shape the size class structure, biodiversity and behavior (diurnal vertical migration) of zooplankton communities. These newly-generated image and metabarcoding datasets of the mesozooplankton community from 0-1000 m are cross-comparable with other ocean regions. These data describe how migratory and midwater resident zooplankton communities are structured by environmental variables and demonstrate how this influences their biogeochemical contributions (specifically active flux and midwater attenuation of flux). Data tools generated for the image analysis in combination with metabarcoding has broad application in plankton ecology and allows metanalysis of other datasets. The project is complementary to ongoing national and international projects that seek to describe the function and structure of the midwater. In contrast to existing modeling and process projects, this project covers a moderately large geographic area and thus provides a strong comparative foundation for broader community-wide assessment of the function of zooplankton in the twilight zone.</p>
<p>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>
Zooplankton Gradients
largerWorkCitation
project
eng; USA
oceans
western North Atlantic, 35-50 degrees North; transect between 35 and 50N along CLIVAR line P17N
-134.979
-52.0707
33.5052
50.0913
2011-08-13
2022-01-01
North Atlantic and North Pacific
0
BCO-DMO catalogue of parameters from ZooProcess and Ecotaxa output from ZooSCANs of zooplankton collected along physical gradients during OAPS MOCNESS tows during R/V Oceanus northwest Atlantic 2011 cruise OC473 and R/V New Horizon northeast Pacific 2012 cruise NH1208 and imaged in 2021-2022
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/938387.rdf
Name: object_id
Units: unitless
Description: <p>Particle identification number. Typically cruiseID_mocnessID_net#_taxonomy_image#. [Source: User]</p>
http://lod.bco-dmo.org/id/dataset-parameter/938388.rdf
Name: object_lat_start
Units: Decimal degrees
Description: <p>Starting latitude of sample collection. [Source: User]</p>
http://lod.bco-dmo.org/id/dataset-parameter/938389.rdf
Name: object_lon_start
Units: Decimal degrees
Description: <p>Starting longitude of sample collection. [Source: User]</p>
http://lod.bco-dmo.org/id/dataset-parameter/938390.rdf
Name: object_date
Units: unitless
Description: <p>Date of sample collection. Local time zone (ADT/AST). [Source: User]</p>
http://lod.bco-dmo.org/id/dataset-parameter/938391.rdf
Name: object_time
Units: unitless
Description: <p>Start time of sample collection. Local time zone (ADT/AST). [Source: User]</p>
http://lod.bco-dmo.org/id/dataset-parameter/938392.rdf
Name: object_ISO_DateTime_UTC
Units: unitless
Description: <p>Datetime with timezone (start time of sample collection). Format ISO 8601, Time Zone UTC. [Source: User]</p>
http://lod.bco-dmo.org/id/dataset-parameter/938393.rdf
Name: object_link
Units: unitless
Description: <p>URL to Villefranche sur mer Quantitative Imaging Platform which hosts manuals summarizing image capture and upload. Autogenerated by software. [Source: Zooprocess]</p>
http://lod.bco-dmo.org/id/dataset-parameter/938394.rdf
Name: object_depth_min
Units: Meters
Description: <p>Minimum depth of sample collection (Zmin, shallowest net depth). [Source: User]</p>
http://lod.bco-dmo.org/id/dataset-parameter/938395.rdf
Name: object_depth_max
Units: Meters
Description: <p>Maximum depth of sample collection (Zmax, deepest net depth). [Source: User]</p>
http://lod.bco-dmo.org/id/dataset-parameter/938396.rdf
Name: object_lat_end
Units: Decimal degrees
Description: <p>Ending latitude of sample collection. [Source: User]</p>
http://lod.bco-dmo.org/id/dataset-parameter/938397.rdf
Name: object_lon_end
Units: Decimal degrees
Description: <p>Ending longitude of sample collection. [Source: User]</p>
http://lod.bco-dmo.org/id/dataset-parameter/938398.rdf
Name: object_area
Units: Square pixels
Description: <p>Surface area of the object. [Source: Zooprocess]</p>
http://lod.bco-dmo.org/id/dataset-parameter/938399.rdf
Name: object_mean
Units: pixel intensity
Description: <p>Average grey value within the object. Pixel intensity value 0-255 (8 bit greyscale image).</p>
http://lod.bco-dmo.org/id/dataset-parameter/938400.rdf
Name: object_stddev
Units: pixel intensity
Description: <p>Standard deviation of the grey value used to generate the mean grey value. Pixel intensity value 0-255 (8 bit greyscale image).</p>
http://lod.bco-dmo.org/id/dataset-parameter/938401.rdf
Name: object_mode
Units: pixel intensity
Description: <p>Modal grey value within the object. Pixel intensity value 0-255 (8 bit greyscale image).</p>
http://lod.bco-dmo.org/id/dataset-parameter/938402.rdf
Name: object_min
Units: pixel intensity
Description: <p>Minimum grey value within the object (0=black). Pixel intensity value 0-255 (8 bit greyscale image).</p>
http://lod.bco-dmo.org/id/dataset-parameter/938403.rdf
Name: object_max
Units: pixel intensity
Description: <p>Maximum grey value within the object (255=white). Pixel intensity value 0-255 (8 bit greyscale image).</p>
http://lod.bco-dmo.org/id/dataset-parameter/938404.rdf
Name: object_x
Units: Pixels
Description: <p>X position of the center of gravity of the object within the vignette. [Source: Zooprocess]</p>
http://lod.bco-dmo.org/id/dataset-parameter/938405.rdf
Name: object_y
Units: Pixels
Description: <p>Y position of the center of gravity of the object within the vignette. [Source: Zooprocess]</p>
http://lod.bco-dmo.org/id/dataset-parameter/938406.rdf
Name: object_xm
Units: Pixels
Description: <p>X position of the center of gravity of the object's grey levels within the vignette. [Source: Zooprocess]</p>
http://lod.bco-dmo.org/id/dataset-parameter/938407.rdf
Name: object_ym
Units: Pixels
Description: <p>Y position of the center of gravity of the object's grey levels within the vignette. [Source: Zooprocess]</p>
http://lod.bco-dmo.org/id/dataset-parameter/938408.rdf
Name: object_perim
Units: Pixels
Description: <p>Length of the outside boundary (perimeter) of the object. [Source: Zooprocess]</p>
http://lod.bco-dmo.org/id/dataset-parameter/938409.rdf
Name: object_bx
Units: Pixels
Description: <p>X coordinate of the top left point of the smallest rectangle enclosing the object within the whole scan image. [Source: Zooprocess]</p>
http://lod.bco-dmo.org/id/dataset-parameter/938410.rdf
Name: object_by
Units: Pixels
Description: <p>Y coordinate of the top left point of the smallest rectangle enclosing the object within the whole scan image. [Source: Zooprocess]</p>
http://lod.bco-dmo.org/id/dataset-parameter/938411.rdf
Name: object_width
Units: Pixels
Description: <p>Width of the smallest rectangle enclosing the object. [Source: Zooprocess]</p>
http://lod.bco-dmo.org/id/dataset-parameter/938412.rdf
Name: object_height
Units: Pixels
Description: <p>Height of the smallest rectangle enclosing the object. [Source: Zooprocess]</p>
http://lod.bco-dmo.org/id/dataset-parameter/938413.rdf
Name: object_major
Units: Pixels
Description: <p>Primary axis of the best fitting ellipse for the object. [Source: Zooprocess]</p>
http://lod.bco-dmo.org/id/dataset-parameter/938414.rdf
Name: object_minor
Units: Pixels
Description: <p>Secondary axis of the best fitting ellipse for the object. [Source: Zooprocess]</p>
http://lod.bco-dmo.org/id/dataset-parameter/938415.rdf
Name: object_angle
Units: Decimal degrees
Description: <p>Angle between the primary axis and a line parallel to the x-axis of the image. [Source: Zooprocess]</p>
http://lod.bco-dmo.org/id/dataset-parameter/938416.rdf
Name: object_circ
Units: unitless
Description: <p>Circularity. (4*pi*Area)/Perim^2. A value of 1 indicates a perfect circle, a value approaching 0 indicates an increasingly elongated polygon. . [Source: Zooprocess]</p>
http://lod.bco-dmo.org/id/dataset-parameter/938417.rdf
Name: object_feret
Units: Pixels
Description: <p>Maximum ferret diameter, i.e. the longest distance between any two points along the object boundary. [Source: Zooprocess]</p>
http://lod.bco-dmo.org/id/dataset-parameter/938418.rdf
Name: object_intden
Units: unitless
Description: <p>Integrated density. The sum of the grey values of the pixels in the object (i.e. = Area*Mean). . [Source: Zooprocess]</p>
http://lod.bco-dmo.org/id/dataset-parameter/938419.rdf
Name: object_median
Units: pixel intensity
Description: <p>Median grey value within the object. Pixel intensity value 0-255 (8 bit greyscale image). [Source: Zooprocess]</p>
http://lod.bco-dmo.org/id/dataset-parameter/938420.rdf
Name: object_skew
Units: unitless
Description: <p>Skewness (third order moment about the mean) of the histogram of the grey level values. [Source: Zooprocess]</p>
http://lod.bco-dmo.org/id/dataset-parameter/938421.rdf
Name: object_kurt
Units: unitless
Description: <p>Kurtosis (fourth order moment about the mean) of the histogram of grey level values. [Source: Zooprocess]</p>
http://lod.bco-dmo.org/id/dataset-parameter/938422.rdf
Name: object_perc_area
Units: Percentage
Description: <p>Percentage of object's surface area that is comprised of holes, defined as the background grey level. [Source: Zooprocess]</p>
http://lod.bco-dmo.org/id/dataset-parameter/938423.rdf
Name: object_xstart
Units: Pixels
Description: <p>X coordinate of the top left point of the image within the scan. [Source: Zooprocess]</p>
http://lod.bco-dmo.org/id/dataset-parameter/938424.rdf
Name: object_ystart
Units: Pixels
Description: <p>Y coordinate of the top left point of the image within the scan. [Source: Zooprocess]</p>
http://lod.bco-dmo.org/id/dataset-parameter/938425.rdf
Name: object_area_exc
Units: Square pixels
Description: <p>Surface area of the object excluding holes (=Area*(1-(%area/100)). [Source: Zooprocess]</p>
http://lod.bco-dmo.org/id/dataset-parameter/938426.rdf
Name: object_fractal
Units: unitless
Description: <p>Fractal dimension of the object boundary (Berube and Jebrak, 1999). [Source: Zooprocess]</p>
http://lod.bco-dmo.org/id/dataset-parameter/938427.rdf
Name: object_skelarea
Units: Pixels
Description: <p>Surface area of skeleton in pixels. In a binary image, the skeleton is obtained by repeatedly removing pixels from the edges of objects until they are reduced to the width of a single pixel. (Berube and Jebrak, 1999). [Source: Zooprocess]</p>
http://lod.bco-dmo.org/id/dataset-parameter/938428.rdf
Name: object_slope
Units: unitless
Description: <p>Slope of the grey level normalized cumulative histogram. [Source: Zooprocess]</p>
http://lod.bco-dmo.org/id/dataset-parameter/938429.rdf
Name: object_histcum1
Units: pixel intensity
Description: <p>Grey level at 25% of the normalized cumulative histogram of grey levels. [Source: Zooprocess]</p>
http://lod.bco-dmo.org/id/dataset-parameter/938430.rdf
Name: object_histcum2
Units: pixel intensity
Description: <p>Grey level at 50% of the normalized cumulative histogram of grey levels. [Source: Zooprocess]</p>
http://lod.bco-dmo.org/id/dataset-parameter/938431.rdf
Name: object_histcum3
Units: pixel intensity
Description: <p>Grey level at 75% of the normalized cumulative histogram of grey levels. [Source: Zooprocess]</p>
http://lod.bco-dmo.org/id/dataset-parameter/938432.rdf
Name: object_xmg5
Units: Pixels
Description: <p>X position of the center of gravity of the object using a gamma value of 5. [Source: Zooprocess]</p>
http://lod.bco-dmo.org/id/dataset-parameter/938433.rdf
Name: object_ymg5
Units: Pixels
Description: <p>Y position of the center of gravity of the object using a gamma value of 5. [Source: Zooprocess]</p>
http://lod.bco-dmo.org/id/dataset-parameter/938434.rdf
Name: object_nb1
Units: unitless
Description: <p>Number of remaining objects in the image after thresholding on level Histcum 1. [Source: Zooprocess]</p>
http://lod.bco-dmo.org/id/dataset-parameter/938435.rdf
Name: object_nb2
Units: unitless
Description: <p>Number of remaining objects in the image after thresholding on level Histcum 2. [Source: Zooprocess]</p>
http://lod.bco-dmo.org/id/dataset-parameter/938436.rdf
Name: object_nb3
Units: unitless
Description: <p>Number of remaining objects in the image after thresholding on level Histcum 3. [Source: Zooprocess]</p>
http://lod.bco-dmo.org/id/dataset-parameter/938437.rdf
Name: object_compentropy
Units: unitless
Description: <p>always set to 0, measurement no longer perfomed in Zooprocess. [Source: Zooprocess]</p>
http://lod.bco-dmo.org/id/dataset-parameter/938438.rdf
Name: object_compmean
Units: unitless
Description: <p>always set to 0, measurement no longer perfomed in Zooprocess. [Source: Zooprocess]</p>
http://lod.bco-dmo.org/id/dataset-parameter/938439.rdf
Name: object_compslope
Units: unitless
Description: <p>always set to 0, measurement no longer perfomed in Zooprocess. [Source: Zooprocess]</p>
http://lod.bco-dmo.org/id/dataset-parameter/938440.rdf
Name: object_compm1
Units: unitless
Description: <p>always set to 0, measurement no longer perfomed in Zooprocess. [Source: Zooprocess]</p>
http://lod.bco-dmo.org/id/dataset-parameter/938441.rdf
Name: object_compm2
Units: unitless
Description: <p>always set to 0, measurement no longer perfomed in Zooprocess. [Source: Zooprocess]</p>
http://lod.bco-dmo.org/id/dataset-parameter/938442.rdf
Name: object_compm3
Units: unitless
Description: <p>always set to 0, measurement no longer perfomed in Zooprocess. [Source: Zooprocess]</p>
http://lod.bco-dmo.org/id/dataset-parameter/938443.rdf
Name: object_symetrieh
Units: unitless
Description: <p>Bilateral horizonal symmetry index (Romagnan et al 2016). [Source: Zooprocess]</p>
http://lod.bco-dmo.org/id/dataset-parameter/938444.rdf
Name: object_symetriev
Units: unitless
Description: <p>Bilateral vertical symmetry index (Romagnan et al 2016). [Source: Zooprocess]</p>
http://lod.bco-dmo.org/id/dataset-parameter/938445.rdf
Name: object_symetriehc
Units: unitless
Description: <p>Symmetry of the object in relation to the horizontal axis after thresholding the grey level at Histcum 1 value. [Source: Zooprocess]</p>
http://lod.bco-dmo.org/id/dataset-parameter/938446.rdf
Name: object_symetrievc
Units: unitless
Description: <p>Symmetry of the object in relation to the vertical axis after thresholding at grey level Histcum 1 value. [Source: Zooprocess]</p>
http://lod.bco-dmo.org/id/dataset-parameter/938447.rdf
Name: object_convperim
Units: Pixels
Description: <p>The perimeter of the smallest polygon within which all points of the object fit. [Source: Zooprocess]</p>
http://lod.bco-dmo.org/id/dataset-parameter/938448.rdf
Name: object_convarea
Units: Pixels
Description: <p>The area of the smallest polygon within which all points of the object fit. [Source: Zooprocess]</p>
http://lod.bco-dmo.org/id/dataset-parameter/938449.rdf
Name: object_fcons
Units: unitless
Description: <p>Measure of contrast based on the texture feature descriptor (Amadasun and King, 1989). [Source: Zooprocess]</p>
http://lod.bco-dmo.org/id/dataset-parameter/938450.rdf
Name: object_thickr
Units: unitless
Description: <p>Thickness ratio; relationship between the maximum thickness of an object and the average thickness of the object excluding the maximum. . [Source: Zooprocess]</p>
http://lod.bco-dmo.org/id/dataset-parameter/938451.rdf
Name: object_tag
Units: unitless
Description: <p>Old variable which is no longer used (0 or 1; 1 if duplicate "tagged" object). [Source: Zooprocess]</p>
http://lod.bco-dmo.org/id/dataset-parameter/938452.rdf
Name: object_esd
Units: Pixels
Description: <p>Equivalent spherical diameter. Sqrt(area/?). [Source: Zooprocess]</p>
http://lod.bco-dmo.org/id/dataset-parameter/938453.rdf
Name: object_elongation
Units: unitless
Description: <p>Elongation index. Major axis/minor axis. [Source: Zooprocess]</p>
http://lod.bco-dmo.org/id/dataset-parameter/938454.rdf
Name: object_range
Units: pixel intensity
Description: <p>Range of grey values (0-255). [Source: Zooprocess]</p>
http://lod.bco-dmo.org/id/dataset-parameter/938455.rdf
Name: object_meanpos
Units: unitless
Description: <p>Relative position of the mean grey. (Mean grey- Max grey)/(Mean grey-Min grey). [Source: Zooprocess]</p>
http://lod.bco-dmo.org/id/dataset-parameter/938456.rdf
Name: object_centroids
Units: Pixels
Description: <p>Difference between the mass and the grey-level object's centroids. Square root ((objGreyX - objX)^2 + (objGreyY - objY)^2). [Source: Zooprocess]</p>
http://lod.bco-dmo.org/id/dataset-parameter/938457.rdf
Name: object_cv
Units: unitless
Description: <p>Coefficient of variation of grey values. 100*(stddev/mean). [Source: Zooprocess]</p>
http://lod.bco-dmo.org/id/dataset-parameter/938458.rdf
Name: object_sr
Units: unitless
Description: <p>Index of variation of grey values. 100*(stddev/max-min)). [Source: Zooprocess]</p>
http://lod.bco-dmo.org/id/dataset-parameter/938459.rdf
Name: object_perimareaexc
Units: unitless
Description: <p>Index of relative complexity of the perimeter. perimeter/area_exc. [Source: Zooprocess]</p>
http://lod.bco-dmo.org/id/dataset-parameter/938460.rdf
Name: object_feretareaexc
Units: unitless
Description: <p>Alternate elongation index. feret/area_exc. [Source: Zooprocess]</p>
http://lod.bco-dmo.org/id/dataset-parameter/938461.rdf
Name: object_perimferet
Units: unitless
Description: <p>Index of relative complexity of the perimeter. perim/feret. [Source: Zooprocess]</p>
http://lod.bco-dmo.org/id/dataset-parameter/938462.rdf
Name: object_perimmajor
Units: unitless
Description: <p>Alternate index of relative complexity of the perimeter. perim/major. [Source: Zooprocess]</p>
http://lod.bco-dmo.org/id/dataset-parameter/938463.rdf
Name: object_circex
Units: unitless
Description: <p>Circularity of the object excluding white pixels. (4*pi(?)*area_exc)/perimeter^2. [Source: Zooprocess]</p>
http://lod.bco-dmo.org/id/dataset-parameter/938464.rdf
Name: object_cdexc
Units: Pixels
Description: <p>Distance between the mass and the grey-level object's centroids. (centroid^2)/area_exc. [Source: Zooprocess]</p>
http://lod.bco-dmo.org/id/dataset-parameter/938465.rdf
Name: sample_id
Units: unitless
Description: <p>Name of sample (scan) from which the object originates (image_name without .tif extension). [Source: User]</p>
http://lod.bco-dmo.org/id/dataset-parameter/938466.rdf
Name: sample_dataportal_descriptor
Units: unitless
Description: <p>Optional descriptor. [Source: User]</p>
http://lod.bco-dmo.org/id/dataset-parameter/938467.rdf
Name: sample_scan_operator
Units: unitless
Description: <p>Initials of the individual who performed the scan. [Source: User]</p>
http://lod.bco-dmo.org/id/dataset-parameter/938468.rdf
Name: sample_ship
Units: unitless
Description: <p>Research vessel (if applicable) where sample was taken. [Source: User]</p>
http://lod.bco-dmo.org/id/dataset-parameter/938469.rdf
Name: sample_program
Units: unitless
Description: <p>Research program (if applicable) under which sample was taken. [Source: User]</p>
http://lod.bco-dmo.org/id/dataset-parameter/938470.rdf
Name: sample_stationid
Units: unitless
Description: <p>Station identifier (if applicable) at which sample was taken. [Source: User]</p>
http://lod.bco-dmo.org/id/dataset-parameter/938471.rdf
Name: sample_bottomdepth
Units: Meters
Description: <p>Recorded depth of the seafloor at the start of the tow. [Source: User]</p>
http://lod.bco-dmo.org/id/dataset-parameter/938472.rdf
Name: sample_ctdrosettefilename
Units: unitless
Description: <p>Associated CTD file name (if applicable). [Source: User]</p>
http://lod.bco-dmo.org/id/dataset-parameter/938473.rdf
Name: sample_other_ref
Units: unitless
Description: <p>Optional other reference notes. [Source: User]</p>
http://lod.bco-dmo.org/id/dataset-parameter/938474.rdf
Name: sample_tow_nb
Units: Count
Description: <p>Number of tows, if more than one, combined to create sample. [Source: User]</p>
http://lod.bco-dmo.org/id/dataset-parameter/938475.rdf
Name: sample_tow_type
Units: unitless
Description: <p>Type of tow profile used to collect sample. 1= oblique, 2 = horizontal, 3=vertical, 0= Other sampling method. [Source: User]</p>
http://lod.bco-dmo.org/id/dataset-parameter/938476.rdf
Name: sample_net_type
Units: unitless
Description: <p>Type of net used to collect the sample (e.g. MOCNESS, Reeve, Tucker, etc). [Source: User]</p>
http://lod.bco-dmo.org/id/dataset-parameter/938477.rdf
Name: sample_net_mesh
Units: Microns
Description: <p>Mesh size of the net used to collect the sample. [Source: User]</p>
http://lod.bco-dmo.org/id/dataset-parameter/938478.rdf
Name: sample_net_surf
Units: Meters squared
Description: <p>Area of net mouth. [Source: User]</p>
http://lod.bco-dmo.org/id/dataset-parameter/938479.rdf
Name: sample_zmax
Units: Meters
Description: <p>Maximum depth of tow or net for this sample. [Source: User]</p>
http://lod.bco-dmo.org/id/dataset-parameter/938480.rdf
Name: sample_zmin
Units: Meters
Description: <p>Minimum depth of tow or net for this sample. [Source: User]</p>
http://lod.bco-dmo.org/id/dataset-parameter/938481.rdf
Name: sample_tot_vol
Units: Meters cubed
Description: <p>Total volume of water filtered while capturing this sample. [Source: User]</p>
http://lod.bco-dmo.org/id/dataset-parameter/938482.rdf
Name: sample_comment
Units: unitless
Description: <p>Optional comment on this sample. [Source: User]</p>
http://lod.bco-dmo.org/id/dataset-parameter/938483.rdf
Name: sample_tot_vol_qc
Units: unitless
Description: <p>Quality flag for how volume of this tow or net was acquired. 1= RECORDED volume (flowmeter), 2= Calculated volume (using the mean volumne of other nets, 3= Estimated volume (net area * tow distance) . [Source: User]</p>
http://lod.bco-dmo.org/id/dataset-parameter/938484.rdf
Name: sample_depth_qc
Units: unitless
Description: <p>Quality flag for how the depth of this tow or net was acquired. 1= Measured by a depth sensor, 2= Calculated from cable length and angle, 3= Estimated from cable length. [Source: User]</p>
http://lod.bco-dmo.org/id/dataset-parameter/938485.rdf
Name: sample_sample_qc
Units: unitless
Description: <p>Quality flag for condition of the sample at time of scanning. Set of four digits defined below.; First digit is sample airtightness. 1=OK, 2=NOK (not ok); Second digit is sample richness. 1= Normal richness, 2=Very rich sample, 3=No plankton (almost) in sample; Third digit is sample condition. 1= Good condition , 2 = Dryed (no remaining liquid), 3= Rotton (loss of fixative); Fourth digit is disturbing elements. 1=No disturbing elements, 2=One of few large objects present in jar, 3=SOUP (phytoplankton, organic matter, clay/mud/mineral); . [Source: User]</p>
http://lod.bco-dmo.org/id/dataset-parameter/938486.rdf
Name: sample_barcode
Units: unitless
Description: <p>Barcode number assigned to sample if applicable. [Source: User]</p>
http://lod.bco-dmo.org/id/dataset-parameter/938487.rdf
Name: sample_duration
Units: Minutes
Description: <p>Duration of the sampling tow. [Source: User]</p>
http://lod.bco-dmo.org/id/dataset-parameter/938488.rdf
Name: sample_ship_speed
Units: Knots
Description: <p>Average ship speed during tow. [Source: User]</p>
http://lod.bco-dmo.org/id/dataset-parameter/938489.rdf
Name: sample_cable_length
Units: Meters
Description: <p>Maximum cable out during tow (m). [Source: User]</p>
http://lod.bco-dmo.org/id/dataset-parameter/938490.rdf
Name: sample_cable_angle
Units: Degrees
Description: <p>Angle of the net cable during the tow (degrees from vertical). [Source: User]</p>
http://lod.bco-dmo.org/id/dataset-parameter/938491.rdf
Name: sample_cable_speed
Units: Meters per minute
Description: <p>Speed of the winch payout/retrival during the tow. [Source: User]</p>
http://lod.bco-dmo.org/id/dataset-parameter/938492.rdf
Name: sample_nb_jar
Units: unitless
Description: <p>Number of the jar containing the sample. [Source: User]</p>
http://lod.bco-dmo.org/id/dataset-parameter/938493.rdf
Name: sample_open
Units: unitless
Description: <p>Undefined. [Source: User]</p>
http://lod.bco-dmo.org/id/dataset-parameter/938494.rdf
Name: process_id
Units: unitless
Description: <p>Process identifier. "zooprocess" and then the sample ID. [Source: Zooprocess]</p>
http://lod.bco-dmo.org/id/dataset-parameter/938495.rdf
Name: process_date
Units: unitless
Description: <p>Date the scan was performed. Local time zone (ADT/AST). [Source: Zooprocess]</p>
http://lod.bco-dmo.org/id/dataset-parameter/938496.rdf
Name: process_time
Units: unitless
Description: <p>Time the scan was performed. Local time zone (ADT/AST). [Source: Zooprocess].</p>
http://lod.bco-dmo.org/id/dataset-parameter/938497.rdf
Name: process_img_software_version
Units: unitless
Description: <p>Version of zooprocess software utilized. [Source: Zooprocess]</p>
http://lod.bco-dmo.org/id/dataset-parameter/938498.rdf
Name: process_img_resolution
Units: Dpi
Description: <p>Resolution of the scan. [Source: Zooprocess]</p>
http://lod.bco-dmo.org/id/dataset-parameter/938499.rdf
Name: process_img_od_grey
Units: unitless
Description: <p>Parameter not used- always nan. [Source: Zooprocess]</p>
http://lod.bco-dmo.org/id/dataset-parameter/938500.rdf
Name: process_img_od_std
Units: unitless
Description: <p>Parameter not used- always 0. [Source: Zooprocess]</p>
http://lod.bco-dmo.org/id/dataset-parameter/938501.rdf
Name: process_img_background_img
Units: unitless
Description: <p>Image name of background scan used. [Source: Zooprocess]</p>
http://lod.bco-dmo.org/id/dataset-parameter/938502.rdf
Name: process_particle_version
Units: unitless
Description: <p>Version of zooprocess software used to process particles. [Source: Zooprocess]</p>
http://lod.bco-dmo.org/id/dataset-parameter/938503.rdf
Name: process_particle_threshold
Units: pixel intensity
Description: <p>8 bit coded grey level value to separate the objects from the background. [Source: Zooprocess]</p>
http://lod.bco-dmo.org/id/dataset-parameter/938504.rdf
Name: process_particle_pixel_size_mm
Units: Pixels per millimeter
Description: <p>The number of pixels per millimeter with this dpi. [Source: Zooprocess]</p>
http://lod.bco-dmo.org/id/dataset-parameter/938505.rdf
Name: process_particle_min_size_mm
Units: Millimeters
Description: <p>Minimum size particle included in vignette extraction. [Source: Zooprocess]</p>
http://lod.bco-dmo.org/id/dataset-parameter/938506.rdf
Name: process_particle_max_size_mm
Units: Millimeters
Description: <p>Maximum size particle included in vignette extraction. [Source: Zooprocess]</p>
http://lod.bco-dmo.org/id/dataset-parameter/938507.rdf
Name: process_particle_sep_mask
Units: unitless
Description: <p>Whether or not to include a separation mask created during separation of touching vignettes. [Source: Zooprocess]</p>
http://lod.bco-dmo.org/id/dataset-parameter/938508.rdf
Name: process_particle_bw_ratio
Units: unitless
Description: <p>ratio of pixels from the image that are above the threshold value (i.e; objects of image noise). [Source: Zooprocess]</p>
http://lod.bco-dmo.org/id/dataset-parameter/938509.rdf
Name: process_software
Units: unitless
Description: <p>Software name, version, and date used to process this sample. [Source: Zooprocess]</p>
http://lod.bco-dmo.org/id/dataset-parameter/938510.rdf
Name: acq_id
Units: unitless
Description: <p>Name of the fraction or replicate being imaged (format fraction_cruise_mocness_net). [Source: Zooprocess]</p>
http://lod.bco-dmo.org/id/dataset-parameter/938511.rdf
Name: acq_instrument
Units: unitless
Description: <p>Type of instrument used to take original image (e.g. Zooscan, UVP, etc). [Source: User]</p>
http://lod.bco-dmo.org/id/dataset-parameter/938512.rdf
Name: acq_min_mesh
Units: Microns
Description: <p>The minimum mesh size/minimum hypothetical particle size of the fraction being imaged. [Source: User]</p>
http://lod.bco-dmo.org/id/dataset-parameter/938513.rdf
Name: acq_max_mesh
Units: Microns
Description: <p>The maximum mesh size/maximum hypothetical particle size of the fraction being imaged. [Source: User]</p>
http://lod.bco-dmo.org/id/dataset-parameter/938514.rdf
Name: acq_sub_part
Units: Integer
Description: <p>Portion of the sample in this image- denominator of the ratio (e.g. 1/64 will read "64"). [Source: User]</p>
http://lod.bco-dmo.org/id/dataset-parameter/938515.rdf
Name: acq_sub_method
Units: unitless
Description: <p>Method or splitter type used to subsample (e.g. Motoda, folsom). [Source: User]</p>
http://lod.bco-dmo.org/id/dataset-parameter/938516.rdf
Name: acq_hardware
Units: unitless
Description: <p>Hardware used to image the sample including version number (Zooscan model). [Source: Zooprocess]</p>
http://lod.bco-dmo.org/id/dataset-parameter/938517.rdf
Name: acq_software
Units: unitless
Description: <p>Software used to take the image- Vuescan version number. [Source: Zooprocess]</p>
http://lod.bco-dmo.org/id/dataset-parameter/938518.rdf
Name: acq_author
Units: unitless
Description: <p>Initials of individual who took the image. [Source: Zooprocess]</p>
http://lod.bco-dmo.org/id/dataset-parameter/938519.rdf
Name: acq_imgtype
Units: unitless
Description: <p>Type of image (e.g. zooscan, UVP). . [Source: Zooprocess]</p>
http://lod.bco-dmo.org/id/dataset-parameter/938520.rdf
Name: acq_scan_date
Units: unitless
Description: <p>Date that the scan was performed. Local time zone (ADT/AST). [Source: Zooprocess]</p>
http://lod.bco-dmo.org/id/dataset-parameter/938521.rdf
Name: acq_scan_time
Units: unitless
Description: <p>Time the scan was performed. Local time zone (ADT/AST). [Source: Zooprocess]</p>
http://lod.bco-dmo.org/id/dataset-parameter/938522.rdf
Name: acq_quality
Units: unitless
Description: <p>Parameter not used- always nan. [Source: Zooprocess]</p>
http://lod.bco-dmo.org/id/dataset-parameter/938523.rdf
Name: acq_bitpixel
Units: unitless
Description: <p>Flag- Vuescan coding of the grey resolution for the raw image. [Source: Zooprocess]</p>
http://lod.bco-dmo.org/id/dataset-parameter/938524.rdf
Name: acq_greyfrom
Units: unitless
Description: <p>Flag- The green channel of image from the scanner sensor is converted in grey by Vuescan for the image saving and processing. [Source: Zooprocess]</p>
http://lod.bco-dmo.org/id/dataset-parameter/938525.rdf
Name: acq_scan_resolution
Units: unitless
Description: <p>Flag- Vuescan coding of the resolution, utilized by Zooprocess to compute the pixel size and image resolution in dpi. [Source: Zooprocess]</p>
http://lod.bco-dmo.org/id/dataset-parameter/938526.rdf
Name: acq_rotation
Units: unitless
Description: <p>Flag- The raw image from the scanner is rotated before being saved. [Source: Zooprocess]</p>
http://lod.bco-dmo.org/id/dataset-parameter/938527.rdf
Name: acq_miror
Units: unitless
Description: <p>Flag- The raw image from the scanner is mirrored before being saved. [Source: Zooprocess]</p>
http://lod.bco-dmo.org/id/dataset-parameter/938528.rdf
Name: acq_xsize
Units: Pixels
Description: <p>Horizontal size of the scan. [Source: Zooprocess]</p>
http://lod.bco-dmo.org/id/dataset-parameter/938529.rdf
Name: acq_ysize
Units: Pixels
Description: <p>Vertical size of the scan. [Source: Zooprocess]</p>
http://lod.bco-dmo.org/id/dataset-parameter/938530.rdf
Name: acq_xoffset
Units: Pixels
Description: <p>Scan frame X offset, from scanner factory calibration. [Source: Zooprocess]</p>
http://lod.bco-dmo.org/id/dataset-parameter/938531.rdf
Name: acq_yoffset
Units: Pixels
Description: <p>Scan frame Y offset, from scanner factory calibration. [Source: Zooprocess]</p>
http://lod.bco-dmo.org/id/dataset-parameter/938532.rdf
Name: acq_lut_color_balance
Units: unitless
Description: <p>Indicates that the raw image normalisation will be done by Zooprocess. [Source: Zooprocess]</p>
http://lod.bco-dmo.org/id/dataset-parameter/938533.rdf
Name: acq_lut_filter
Units: unitless
Description: <p>If there is a filter in the acquisition LUT (all should be "no"). [Source: Zooprocess]</p>
http://lod.bco-dmo.org/id/dataset-parameter/938534.rdf
Name: acq_lut_min
Units: pixel intensity
Description: <p>Minimum 16 bit coded grey level utilized for the 16 to 8 bit raw image conversion/normalisation by Zooprocess. [Source: Zooprocess]</p>
http://lod.bco-dmo.org/id/dataset-parameter/938535.rdf
Name: acq_lut_max
Units: pixel intensity
Description: <p>Maximum 16 bit coded grey level utilized for the 16 to 8 bit raw image conversion/normalisation by Zooprocess. [Source: Zooprocess]</p>
http://lod.bco-dmo.org/id/dataset-parameter/938536.rdf
Name: acq_lut_odrange
Units: unitless
Description: <p>Optical Density range for the 16 to 8 bit raw image conversion/normalisation by Zooprocess (always 1.8). [Source: Zooprocess]</p>
http://lod.bco-dmo.org/id/dataset-parameter/938537.rdf
Name: acq_lut_ratio
Units: unitless
Description: <p>ratio applied to the acq_lut_max value for the 16 to 8 bit raw image conversion/normalisation by Zooprocess (always 1.15). [Source: Zooprocess]</p>
http://lod.bco-dmo.org/id/dataset-parameter/938538.rdf
Name: acq_lut_16b_median
Units: pixel intensity
Description: <p>Measured median grey level of the raw image. [Source: Zooprocess]</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
675739842
https://darchive.mblwhoilibrary.org/server/api/core/bitstreams/28a6bf7d-f67f-4d11-becd-f0f058e003c8/content
download
https://doi.org/10.26008/1912/bco-dmo.932252.1
download
onLine
dataset
<div>
<p><strong>Location:&nbsp;</strong></p>
<p>Northwestern Atlantic, 0 to 1000m depth, 35N, 52W to 50N, 42W along CLIVAR/WOCE line A20<br />
Northeastern Pacific, 0 to 1000m depth, 50N, 150W to 35N, 135W along CLIVAR/WOCE line P17N<br />
<br />
<strong>Methodology:&nbsp;</strong></p>
<p>To obtain samples, a 1m<sup>2</sup>&nbsp;Multiple Opening/Closing Net and Environmental Sensing System &nbsp;(MOCNESS; Wiebe et al., 1985) equipped with nine 150 m nets was deployed during the mid-day and mid-night on cruises carried out as described in &nbsp;<a href="https://www.bco-dmo.org/dataset/3546" style="box-sizing: inherit; color: rgb(0, 102, 153); cursor: pointer; text-decoration-line: none; vertical-align: baseline; margin: 0px; padding: 0px; border: 0px; font: inherit;"><u>https://www.bco-dmo.org/dataset/3546</u></a>. Briefly, sampling was at consistent intervals including 1000-800, 800-600, 600-400, 400-200, 200-100, 100-50, 50-25, 25-0m at day/night stations from 35 to 50 N in the northwest Atlantic in 2011, and from 35 and 50N along CLIVAR line P17N &nbsp;in 2012.</p>
<p>Upon retrieval, the catch from each of the eight discrete nets were divided into splits. One-half of a sample was preserved in 95% ethanol, one quarter was preserved in 5% buffered formalin, and one quarter was used for live viewing and picking, and then preserved in 70% ethanol.</p>
<p>A representative subsample of the formalin-preserved zooplankton community from each net were imaged using a ZooSCAN ver. 4 at&nbsp; either 4,800 dpi with a narrow frame, or 2400 dpi with a large frame (following the methods in: Gorsky et al., 2010, Vandromme et al., 2012, as detailed in Maas et al. 2021). Scanning resolution was changed partway through the project in accordance with advice from Hydroptic (written communication). In order to better represent all size classes in the images, the original sample was divided into three size categories. All individuals larger than 2 cm were selected by eye and scanned separately from all the others ("d1"). The remainder of the sample was sieved through a 1-mm mesh sieve, and both size fractions ("d2" &gt;1000um but excluding d1; "d3" between 150-1000um) were individually scanned. From these smaller size fractions, at least 1500 particles were scanned after subsampling using a Motoda splitter (Motoda, 1959), requiring generation of two separate scans for both size classes. This resulted in a total of five images per net.</p>
</div>
<div>
<p><strong>ZooSCAN&nbsp;Image names:</strong><br />
<br />
<span style="font-size:13px">Image names&nbsp;include:&nbsp;</span>cruise#_mocnessID_net#_sizefraction_ and _a|b if a replicate and end in _1.tif<br />
<br />
<span style="font-size:13px">Multiple images of the same size fraction were sometimes taken to obtain a sufficient number of particles. These replicates are named a or b. If there is no replicate they don’t have a letter in the image name. An a and b scan were always done for size classes d2 and d3.&nbsp; This was important because the split size is for the sum of a+b (e.g. if a is ¼ and b is ¼, the acq_sub_part will be 0.5).<br />
<br />
<strong>Example of ZooSCAN image names:</strong></span></p>
<p><span style="font-size:13px">ae1830_m13_n4_d3_a_1.tif&nbsp; [a replicate]<br />
ae1830_m13_n4_d3_b_1.tif&nbsp;&nbsp;</span>[a replicate]<br />
<span style="font-size:13px">ae1830_m13_n5_d1_1.tif&nbsp; &nbsp; &nbsp; </span>[no&nbsp;replicate]<br />
<br />
The "object_id" in this dataset (the particle identifier)&nbsp; is constructed the same way as the ZooSCAN image name except it as an additional _#&nbsp;at the end.&nbsp; This additional number in the object_id is added by the ZooProcess software (Hydroptic, 2016).<br />
e.g.<br />
object_id:&nbsp; &nbsp; &nbsp; &nbsp;ae1614_m3_n1_d2_a_1<strong>_100</strong><br />
image_name: ae1614_m3_n1_d2_a_1.tif</p>
<p><strong>Particle names:</strong></p>
<p>Names for particles (objects) follow the pattern "CruiseID_MocnessID_NetNumber_ScanFraction" followed by "_1_XXX", with "1" being automatically added by the software to indicate no duplicates of that scan and "XXX" being the unique particle number within that scan.&nbsp;<br />
<br />
<strong>Parameter (column name) nomenclature and data origin:&nbsp;<br />
* </strong>(see&nbsp;the "Parameters" section which contains all column information for the ecotaxa output table)</p>
<p>Parameters (column names)&nbsp;beginning with "object" include basic identifying metadata input by the user as well as all particle measurement data generated by ZooProcess. Any parameters beginning with "object_annotation" parameters are added by Ecotaxa. Parameters that begin with "sample" are sampling metadata input by the user during the scanning process.&nbsp; "Process" parameters describe the software and assumptions or corrections input during the data processing. "Acq" describes the portion of the sample scanned (input by user) and provides some summary data about the scanned image.&nbsp;</p>
<p><strong>Interpreting acq_sub_part</strong></p>
<p>The acq_sub_part is the denominator of the fraction of the sample scanned (e.g. "8" would be 1/8 or 0.125). For this project, the acq sub part is the fraction of the&nbsp;<u>whole size fraction</u>. "A" and "B" scans of the same fraction are considered to be halves of the whole fraction and can be statistically lumped together (e.g. if d2_a and d2_b from the same net were each 0.25 ("4") of that size fraction, the acq sub part will be 0.5 ("2").&nbsp;<br />
<br />
<span style="font-size:14px"><strong>Instruments summaries:</strong></span></p>
<p><strong>MOCNESS</strong></p>
<p>The Multiple Opening/Closing Net and Environmental Sensing System or MOCNESS is a family of net systems based on the Tucker Trawl principle. There are currently 8 different sizes of MOCNESS in existence which are designed for capture of different size ranges of zooplankton and micro-nekton. Each system is designated according to the size of the net mouth opening and in two cases, the number of nets it carries. The original MOCNESS (Wiebe et al, 1976) was a redesigned and improved version of a system described by Frost and McCrone (1974)(from MOCNESS manual). These nets allow for the discrete sampling of zooplankton at targeted depths while simultaneously capturing data on physical parameters. The MOCNESS used in all sampling for both cruises was a 1m<sup>2</sup>&nbsp;(mouth size) rigged as below.&nbsp;</p>
<p><strong>From OC473 Cruise Report </strong>(Lawson, et al. (2011),&nbsp;http://hdl.handle.net/1834/43091):</p>
<p>"The MOCNESS was equipped with eight 150-um mesh nets (nets 1-8; borrowed from URI) and one 333-um mesh net (net 0). The underwater unit used was #169. In addition to the standard temperature and conductivity probes the system also had a beta-type strobe-light unit for reducing avoidance of the nets by some zooplankton and possibly small fish.&nbsp; The strobe system has two units each with 12 LED sets (LUXEON Rebel LED) with peak output between 490-520 nm. Seven of the 24 LED sets were no longer working at the start of the sampling. The LEDs are powered by the MOCNESS battery and their pulse width, amplitude, flash rate period, and on/off are controlled by the MOCNESS software. For this cruise the pulse width was 2 ms, the relative amplitude was 99%, and the flash interval was 100 ms."</p>
<p><strong>From NH1208 Cruise Report</strong> (Lawson, et al. (2012), http://hdl.handle.net/1834/43090):</p>
<p>"The MOCNESS was equipped with eight 150-um mesh nets (nets 1-8; borrowed from URI) and one 333-um mesh net (net 0). The system was equipped with the standard SeaBird&nbsp; temperature and conductivity probes (units #535 and #120 respectively). The underwater unit used was #169. In addition to the standard temperature and conductivity probes the system also had a beta-type strobe-light unit for reducing avoidance of the nets by some zooplankton and possibly small fish.&nbsp; The strobe system has two units each with 12 LED sets (LUXEON Rebel LED) with peak output between 490-520 nm. Seven of the 24 LED sets were no longer working at the start of the sampling. The LEDs are powered by the MOCNESS battery and their pulse width, amplitude, flash rate period, and on/off are controlled by the MOCNESS software. For this cruise the pulse width was 2 ms, the relative amplitude was 99%, and the flash interval was 100 ms. The strobe unit was only used for the first four tows, after which problems with blowing the underwater unit 5A fuse (a symptom typical of strobe unit problems from the past) led us to disconnect it and not use it for the remainder of the tows."</p>
<p><strong>ZOOSCAN</strong></p>
<p>The ZooSCAN (CNRS patent) system makes use of scanner technology with custom lighting and a watertight scanning chamber into which liquid zooplankton samples can be placed. The scanner recovers a high-resolution, digital image and the sample can be recovered without damage.&nbsp; These digital images can then be investigated by computer processing. While the resolution of the digitized zooplankton images is lower than the image obtained using a binocular microscope, this technique has proven to be more than adequate for large sample sets. Identification of species is done by automatic comparison of the image (vignette) of each individual animal in the scanned image with a library data set which may be built by the investigator for each individual survey or imported from a previous survey. The latest machine learning algorithm allows high recognition levels even if we recommend complementary manual sorting to achieve a high number of taxonomic groups.&nbsp;Scans for this dataset performed with a ZooSCAN&nbsp;(Hydroptic, HYDROPTIC_V4) running with Vuescan (version 9.5.24) and ZooProcess (version 8.22, ImageJ macro suite). Images were taken at either 4800dpi with a narrow frame or 2400dpi with a large frame.&nbsp;</p>
</div>
Specified by the Principal Investigator(s)
<p>Scans were processed using ZooProcess (version 8.22, ImageJ macro suite). The "Convert and process from RAW" function was used to separate particles into individual vignettes and generate a suite of measurements for each particle. "Doubles" (vignettes containing more than one particle) were manually separated in the software and reprocessed.&nbsp;<br />
<br />
Example vignettes (see Supplemental files for example image download):<br />
<img alt="Example copepod vignette" src="https://datadocs.bco-dmo.org/file/KA2g6mjHqr8GE3/copepod_6994.jpg" style="border-style:solid; border-width:1px; height:150px; width:224px" />&nbsp;<img alt="Example ostracod vignette" src="https://datadocs.bco-dmo.org/file/OJ2mZqjt564E2q/ostracod_female.jpg" style="border-style:solid; border-width:1px; height:150px; width:200px" />&nbsp;<img alt="Example pteropod vignette" src="https://datadocs.bco-dmo.org/file/xoBpl9WCJvq6vV/thecosome1.jpg" style="border-style:solid; border-width:1px; height:150px; width:83px" /></p>
<p>Processed scans and their corresponding metadata were then uploaded to Ecotaxa (Picheral et al, https://ecotaxa.obs-vlfr.fr/), where a training set was created using manually classified images from this project as well as existing validated images from other projects in the Sargasso Sea. Classification categories were chosen based on taxon of interest, identification level in previous projects, and known limitations of the software. Generally, broader level taxonomic groups are used. Identification of all particles was predicted, then manually validated.&nbsp;</p>
<p><strong>Data versioning</strong></p>
<p>The ecotaxa data included in this dataset version are "Ecotaxa Export version 1.0."</p>
<p>The ecotaxa export file will be updated in a versioned manner as validation of identification is completed.&nbsp; Ecotaxa output versions are as&nbsp;follows:&nbsp;</p>
<p>Version 1: No identifications, predicted or validated<br />
Version 2: All identifications predicted<br />
Version 3: All identifications validated<br />
&nbsp;</p>
Specified by the Principal Investigator(s)
Version 1:
* Data from source file ecotaxa_export_5421_20240614_1445_v1_0.tsv were imported into the BCO-DMO data system as the primary table for this dataset with "nan" values interpreted as missing data identifiers.
* After import, select columns designated to have the missing data identifier 99999 had a find and replace operation performed to turn 99999 values into system missing data identifiers. This was not done on import since only some columns were described as using this identifier by the data providers. 99999 is within the valid numeric range for columns such as object_intden and object_area_exec so it is possible that if there were any real 99999 values, they were instead interpreted as missing data.
** 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.
* There were two sets of lat lon columns called object_lat, object_lon. The metadata described these as the start and end lat,lon of the sampling event. So renamed -> object_lat_start, object_lon_start, object_lat_end, object_lon_end. The values were the same in both sets except some were null in the end set where the start set was 33.50517,-135.
* object_ISO_DateTime_UTC added from local date and time columns.
* extra trailing slash removed in object_link (all values were "http://www.zooscan.obs-vlfr.fr//"). This link may not be persistent for long-term curation, a citation for the site was added as a related publication along with the date it was accessed.
* The following blank columns were removed from this table to be consistent with columns in other ecotaxa table (BCO-DMO dataset 931883).
** object_annotation_status object_annotation_person_name, object_annotation_person_email, object_annotation_date, object_annotation_time, object_annotation_category, object_annotation_hierarchy, complement_info
* Parameters (column names) renamed to comply with BCO-DMO naming conventions. See https://www.bco-dmo.org/page/bco-dmo-data-processing-conventions (% in col name changed to "perc", trailing periods removed).
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
1m MOCNESS
1m MOCNESS
PI Supplied Instrument Name: 1m MOCNESS Instrument Name: MOCNESS1 Instrument Short Name:MOC1 Instrument Description: The Multiple Opening/Closing Net and Environmental Sensing System or MOCNESS is a family of net systems based on the Tucker Trawl principle. The MOCNESS-1 carries nine 1-m2 nets usually of 335 micrometer mesh and is intended for use with the macrozooplankton. All nets are black to reduce contrast with the background. A motor/toggle release assembly is mounted on the top portion of the frame and stainless steel cables with swaged fittings are used to attach the net bar to the toggle release. A stepping motor in a pressure compensated case filled with oil turns the escapement crankshaft of the toggle release which sequentially releases the nets to an open then closed position on command from the surface. -- from the MOCNESS Operations Manual (1999 + 2003). Community Standard Description: http://vocab.nerc.ac.uk/collection/L22/current/NETT0097/
ZooSCAN ver. 4
ZooSCAN ver. 4
PI Supplied Instrument Name: ZooSCAN ver. 4 PI Supplied Instrument Description:http://www.hydroptic.com/index.php/public/Page/product_item/ZOOSCAN
A representative subsample of the formalin-preserved zooplankton community from each net were imaged using a ZooSCAN ver. 4 at either 4,800 dpi with a narrow frame, or 2400 dpi with a large frame (following the methods in: Gorsky et al., 2010, Vandromme et al., 2012, as detailed in Maas et al. 2021).
Scans for this dataset performed with a ZooScan (Hydroptic, HYDROPTIC_V4) running with Vuescan (version 9.5.24) and Zooprocess (version 8.22, ImageJ macro suite). Images were taken at either 4800dpi with a narrow frame or 2400dpi with a large frame. Instrument Name: ZooSCAN Instrument Short Name: Instrument Description: Description excerpt from Hydroptic website
http://www.hydroptic.com/index.php/public/Page/product_item/ZOOSCAN
The ZooSCAN (CNRS patent) system makes use of scanner technology with custom lighting and a watertight scanning chamber into which liquid zooplankton samples can be placed. The scanner recovers a high-resolution, digitial image and the sample can be recovered without damage. These digital images can then be investigated by computer processing. While the resolution of the digitized zooplankton images is lower than the image obtained using a binocular microscope this technique has proved to be more than adequate for large sample sets. Identification of species is done by automatic comparison of the image (vignette) of each individual animal in the scanned image with a library data set which may be built by the investigator for each individual survey or imported from a previous survey. The latest machine learning algorithm allows high recognition levels even if we recommend complementary manual sorting to achieve a high number of taxonomic groups.
Cruise: OC473
OC473
R/V Oceanus
Community Standard Description
International Council for the Exploration of the Sea
R/V Oceanus
vessel
OC473
Gareth Lawson
Woods Hole Oceanographic Institution
http://hdl.handle.net/1834/43091
Report describing OC473
Cruise: NH1208
NH1208
R/V New Horizon
Community Standard Description
International Council for the Exploration of the Sea
R/V New Horizon
vessel
NH1208
Gareth Lawson
Woods Hole Oceanographic Institution
http://hdl.handle.net/1834/43090
Report describing NH1208
R/V Oceanus
Community Standard Description
International Council for the Exploration of the Sea
R/V Oceanus
vessel
R/V New Horizon
Community Standard Description
International Council for the Exploration of the Sea
R/V New Horizon
vessel