http://lod.bco-dmo.org/id/dataset/809515 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 2020-04-16 ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data ISO 19115-2:2009(E) Experiments on orientation of colonial diatom Stephanopyxis turris in Couette flow using hologram imagery analysis 2020-04-16 publication 2020-04-16 revision Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA) 2022-09-30 publication https://doi.org/10.26008/1912/bco-dmo.809515.1 James Sullivan Florida Atlantic University HBOI principalInvestigator Malcolm McFarland Florida Atlantic University HBOI principalInvestigator Aditya Nayak Florida Atlantic University HBOI principalInvestigator Melissa Omand University of Rhode Island principalInvestigator Jan Rines University of Rhode Island 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: Sullivan, J., McFarland, M., Nayak, A., Omand, M., Rines, J. (2022) Experiments on orientation of colonial diatom Stephanopyxis turris in Couette flow using hologram imagery analysis. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2020-04-16 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.809515.1 [access date] Phytoplankton Orientation - Diatom Stephanopyxis Dataset Description: Methods and Sampling: &lt;p&gt;A uni-algal culture of the colonial diatom &lt;em&gt;Stephanopyxis turris&lt;/em&gt; was grown in 2 separate Couette chambers under controlled shear conditions for up to 24 days. The Couette chambers (40 cm height) consisted of an inner rotating cylinder (12.7 cm radius) and an outer stationary cylinder (14.92 cm radius). A laminar flow chamber rotated at 0.5 rpm and a turbulent flow chamber rotated at 13 rpm. The gap between the cylinders was filled with 8 L of sterile L1 medium (Guillard and Hargraves 1993). Experiments took place in a temperature and light controlled walk-in incubator at 20° C with a 12:12 light:dark cycle. Light was provided by cool white fluorescent lamps producing 32 µmol photons m-2 s-1 at the center of each chamber.&lt;/p&gt; &lt;p&gt;Digital holograms through the entire height of each Couette chamber (40 cm) were acquired at 3 day intervals during the duration of the experiment. Each hologram imaged 19.35 mL of water. The total volume imaged and analyzed on each day and for each chamber was 3.9 L representing 202 holograms.&lt;/p&gt; &lt;p&gt;A custom digital holographic microscope (DHM) was constructed to image particles within the Couette chambers. Coherent illumination was provided by a green (532 nm) nanosecond pulsed laser. The incident beam was directed upward through the bottom of the chamber and images were acquired by a CCD camera (4896 x 3264 pixels) positioned above the chamber looking downward through the illuminated volume. An objective lens in front of the camera increased magnification and positioned the hologram image plane at the water surface. Hologram resolution was 1.74 µm/pixel.&lt;/p&gt; &lt;p&gt;Holograms were numerically reconstructed in Matlab (version 2019a) using the Kirchoff-Fresnel convolution kernel (Katz and Sheng 2010) at 1 mm intervals throughout the height of the chamber. Reconstructed images were combined to produce a single extended depth of field (EDF) image for each hologram. These EDF images were segmented with a fixed threshold and particle measurements were obtained through automated region analysis in Matlab. See Nayak et al. 2018 for further details.&lt;/p&gt; Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1657332 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1657332 completed James Sullivan Florida Atlantic University HBOI 772-242-2445 Florida Atlantic University - Harbor Branch Oceanographic Institute 5600 US 1 North Fort Pierce FL 34946 USA jsullivan@fau.edu pointOfContact Malcolm McFarland Florida Atlantic University HBOI 772-242-2234 Florida Atlantic University - Harbor Branch Oceanographic Institute 5600 US 1 North Fort Pierce FL 34946 USA mmcfarland@fau.edu pointOfContact Aditya Nayak Florida Atlantic University HBOI 772-242-6427 Florida Atlantic University - Harbor Branch Oceanographic Institute 5600 US 1 North Fort Pierce FL 34946 USA anayak@fau.edu pointOfContact Melissa Omand University of Rhode Island 401-874-6610 215 S Ferry Rd Narrangsett RI 02882-1197 USA momand@uri.edu pointOfContact Jan Rines University of Rhode Island 401-874-6691 Graduate School of Oceanography South Ferry Road Narragansett RI 02882 USA jrines@uri.edu pointOfContact asNeeded Dataset Version: 1 Unknown Day RPM Colony Orientation_degrees Length_um Width_um Aspect_Ratio Couette chambers theme None, User defined days No BCO-DMO term sample identification angle length width featureType BCO-DMO Standard Parameters Digital inline holographic microscope Taylor-Couette system instrument BCO-DMO Standard Instruments 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. Collaborative Research: Orientation of elongate diatoms as a strategy for light harvesting https://osprey.bco-dmo.org/project/686802 Collaborative Research: Orientation of elongate diatoms as a strategy for light harvesting <p><em>NSF Award Abstract:</em><br /> Phytoplankton have an intimate connection to the hydrodynamic environment in which they live.</p> <p>Previous studies have examined the role that turbulence and shear play in nutrient uptake, patch/layer formation, and predator-prey encounters, but the role of phytoplankton orientation to increase light capture (and ultimately primary production) has been largely overlooked. Compelling evidence of persistent horizontal orientation of chain-forming diatoms, obtained from novel in situ holographic imaging, has led to a hypothesis that in regions of strong stratification, shear flows will lead to systematic horizontal orientation of elongate phytoplankton forms that maximizes their cross-sectional area (and light capture) in the ambient downwelling light field. It has also been suggested that variations in phytoplankton size and shape are fundamental traits conferring selective competitive advantages in certain hydrodynamic environments, thus modifying/mediating community composition. The interdisciplinary research of this project crosses three scientific disciplines (biology, optics and fluid dynamics) and will advance our understanding of the function of diverse forms of phytoplankton, their interactions with fluid flows, and the resultant impacts on the optics of the environment. The project will support a number of undergraduate and graduate students, and post-doctoral researchers.</p> <p>This project combines analysis of previously collected field data with laboratory experiments and modeling. For the field data analysis, phytoplankton orientation is quantified from in situ holographic images of the undisturbed water column along with concurrent high resolution measurements of critical physical (turbulence/shear/stratification) and optical parameters collected from a ship-based holographic bio-physics profiler. In the laboratory, the orientation response of different phytoplankton species and morphologies is evaluated in custom built shear tanks under controlled laminar and turbulent conditions to confirm that elongate forms can orient in certain hydrodynamic environments to maximize light capture. In addition, controlled growth/physiology experiments in various shear tank treatments will explore the effects of orientation on growth, photosynthetic parameters and productivity. Lastly, the project results will be incorporated into a global analysis of observed and modeled physical, bio-optical and ecologically-relevant parameters, to quantify the relevance of this phenomenon to primary production and the carbon cycle.</p> Phytoplankton Orientation largerWorkCitation project eng; USA biota oceans 2019-07-01 2019-07-31 Laboratory based experiments conducted at FAU-HBOI and URI 0 BCO-DMO catalogue of parameters from Experiments on orientation of colonial diatom Stephanopyxis turris in Couette flow using hologram imagery analysis 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/809525.rdf Name: Day Units: days Description: <p>days since inoculation</p> http://lod.bco-dmo.org/id/dataset-parameter/809526.rdf Name: RPM Units: revolutions/minute Description: <p>Couette chamber revolutions per minute</p> http://lod.bco-dmo.org/id/dataset-parameter/809527.rdf Name: Colony Units: none Description: <p>identification number</p> http://lod.bco-dmo.org/id/dataset-parameter/809528.rdf Name: Orientation_degrees Units: degrees Description: <p>Particle angle from direction of flow</p> http://lod.bco-dmo.org/id/dataset-parameter/809529.rdf Name: Length_um Units: micrometers Description: <p>Particle length</p> http://lod.bco-dmo.org/id/dataset-parameter/809530.rdf Name: Width_um Units: micrometers Description: <p>Particle width</p> http://lod.bco-dmo.org/id/dataset-parameter/809531.rdf Name: Aspect_Ratio Units: none Description: <p>ratio of length to width</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 1782584 https://darchive.mblwhoilibrary.org/bitstream/1912/29375/1/dataset-809515_phytoplankton-orientation-diatom-stephanopyxis__v1.tsv download https://doi.org/10.26008/1912/bco-dmo.809515.1 download onLine dataset &lt;p&gt;A uni-algal culture of the colonial diatom &lt;em&gt;Stephanopyxis turris&lt;/em&gt; was grown in 2 separate Couette chambers under controlled shear conditions for up to 24 days. The Couette chambers (40 cm height) consisted of an inner rotating cylinder (12.7 cm radius) and an outer stationary cylinder (14.92 cm radius). A laminar flow chamber rotated at 0.5 rpm and a turbulent flow chamber rotated at 13 rpm. The gap between the cylinders was filled with 8 L of sterile L1 medium (Guillard and Hargraves 1993). Experiments took place in a temperature and light controlled walk-in incubator at 20° C with a 12:12 light:dark cycle. Light was provided by cool white fluorescent lamps producing 32 µmol photons m-2 s-1 at the center of each chamber.&lt;/p&gt; &lt;p&gt;Digital holograms through the entire height of each Couette chamber (40 cm) were acquired at 3 day intervals during the duration of the experiment. Each hologram imaged 19.35 mL of water. The total volume imaged and analyzed on each day and for each chamber was 3.9 L representing 202 holograms.&lt;/p&gt; &lt;p&gt;A custom digital holographic microscope (DHM) was constructed to image particles within the Couette chambers. Coherent illumination was provided by a green (532 nm) nanosecond pulsed laser. The incident beam was directed upward through the bottom of the chamber and images were acquired by a CCD camera (4896 x 3264 pixels) positioned above the chamber looking downward through the illuminated volume. An objective lens in front of the camera increased magnification and positioned the hologram image plane at the water surface. Hologram resolution was 1.74 µm/pixel.&lt;/p&gt; &lt;p&gt;Holograms were numerically reconstructed in Matlab (version 2019a) using the Kirchoff-Fresnel convolution kernel (Katz and Sheng 2010) at 1 mm intervals throughout the height of the chamber. Reconstructed images were combined to produce a single extended depth of field (EDF) image for each hologram. These EDF images were segmented with a fixed threshold and particle measurements were obtained through automated region analysis in Matlab. See Nayak et al. 2018 for further details.&lt;/p&gt; Specified by the Principal Investigator(s) &lt;p&gt;&lt;strong&gt;BCO-DMO Processing Notes:&lt;/strong&gt;&lt;br /&gt; - added conventional header with dataset name, PI name, version date&lt;br /&gt; - modified parameter names to conform with BCO-DMO naming conventions&lt;/p&gt; Specified by the Principal Investigator(s) asNeeded 7.x-1.1 Biological and Chemical Oceanography Data Management Office (BCO-DMO) Unavailable 508-289-2009 WHOI MS#36 Woods Hole MA 02543 USA info@bco-dmo.org http://www.bco-dmo.org Monday - Friday 8:00am - 5:00pm For questions regarding this resource, please contact BCO-DMO via the email address provided. pointOfContact PI Supplied Instrument Name: PI Supplied Instrument Description:A custom digital holographic microscope (DHM) was constructed to image particles within the Couette chambers. Coherent illumination was provided by a green (532 nm) nanosecond pulsed laser. The incident beam was directed upward through the bottom of the chamber and images were acquired by a CCD camera (4896 x 3264 pixels) positioned above the chamber looking downward through the illuminated volume. An objective lens in front of the camera increased magnification and positioned the hologram image plane at the water surface. Hologram resolution was 1.74 um/pixel. Instrument Name: Digital inline holographic microscope Instrument Short Name:DIHM Instrument Description: A Digital Inline Holographic Microscope (DIHM) uses coherent (laser) light and a digital camera to image objects with micrometer scale resolution. A portion of the light scattered by illuminated objects interferes with incident light in a predictable manner. The resulting interference patterns projected onto a two-dimensional plane (i.e. digital camera sensor) are recorded as holograms. These digital holograms are then numerically reconstructed to produce an in-focus image at a given distance from the recording plane. A relatively large illuminated volume (>100 mL) can be reconstructed in this manner to produce a single image with an extended depth of field.  Couette chambers Couette chambers PI Supplied Instrument Name: Couette chambers Instrument Name: Taylor-Couette system Instrument Short Name: Instrument Description: An apparatus composed of two vertically oriented, coaxial cylinders separated by a gap that contains seawater. During operation, the outer cylinder rotates at a prescribed speed causing relative motion between the cylinders and thereby shearing the seawater between them.