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            <gmx:Anchor xlink:href="http://lod.bco-dmo.org/id/dataset/926887.rdf" xlink:actuate="onRequest">Photochemical yield and color score data from short-term heat stress assays performed with with corals collected from sites around Heron Island, southern Great Barrier Reef  in Sept and Oct of 2022</gmx:Anchor>
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            <gco:CharacterString>Cite this dataset as: Barott, K., Brown, K. (2024) Photochemical yield and color score data from short-term heat stress assays performed with with corals collected from sites around Heron Island, southern Great Barrier Reef  in Sept and Oct of 2022. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2024-05-07 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.926887.1 [access date]</gco:CharacterString>
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        <gco:CharacterString>Dataset Description: &amp;lt;p&amp;gt;See the &amp;quot;Related Datasets&amp;quot; section for other closely related data that was also part of the study&amp;amp;nbsp;published in Brown et al., 2024.&amp;amp;nbsp;&amp;amp;nbsp;&amp;lt;/p&amp;gt; Methods and Sampling: &amp;lt;p&amp;gt;Acute heat stress experiment&amp;lt;/p&amp;gt;

&amp;lt;p&amp;gt;A standardized temperature profile was used to measure heat tolerance in corals (e.g., (Voolstra et al. 2020; Cunning et al. 2021; Marzonie et al. 2022; Evensen et al. 2023)) with minor modification in temperature profiles. The climatological maximum monthly mean (MMM) of Heron Reef is 27.3°C (Weeks et al. 2008). A pilot experiment with all three genera indicated no difference in Fv/Fm between MMM, MMM+3°C and MMM+6°C, so the latter two treatments were increased to more accurately assess the decline in performance, such that the five treatments used here included ambient, MMM, MMM+4°C, MMM+6.5°C, and MMM+9°C. Generally, experiments began at ~12:00 with a 3-hr ramp to respective treatment temperatures (23°C, 27.3°C, 31.3°C, 33.8°C, 36.3°C), a 3-hr hold, and a 1-hr ramp down to MMM (Evensen et al. 2023) (Figure S1&amp;amp;nbsp;of&amp;amp;nbsp;Brown et al., 2024). Lights were turned off at the onset of the 1-hr ramp down to correspond with sunset. Due to experimental constraints (space, equipment, and time), only two treatments (n = 1 tank) were performed per day and each site was done in isolation. Accordingly, a complete assay took two days per site, with treatments tested each day selected randomly (Table S1, Figure S1&amp;amp;nbsp;of Brown et al., 2024). A fragment from each coral colony was randomly placed into each treatment, so that all colonies were present in each treatment. Temperatures were controlled using an Apex controller (Neptune Systems). Apex temperature probes were calibrated against a high-precision temperature probe (HANNA HI-98190; accuracy: ±0.4°C at 25°C; resolution: ± 0.10°C) at the onset of the experiment. Temperatures were also recorded using cross-calibrated temperature loggers (HOBO UA-001-64, accuracy: ± 0.29°C at 25°C). Photosynthetically active radiation (PAR) was static and controlled using aquarium lights (NICREW HyperReef LED, Shenzhen NiCai Technology Co.), averaging 250 µmol m-2 sec-1.&amp;amp;nbsp;&amp;lt;/p&amp;gt;

&amp;lt;p&amp;gt;Physiological responses to acute heat stress&amp;lt;/p&amp;gt;

&amp;lt;p&amp;gt;At the end of the ramp and after 1 h of darkness (~19:00), corals were assessed for dark-adapted photochemical yield (Fv/Fm) using a Diving-PAM (Walz GmbH) 5-mm diameter fiber-optic probe at a standardized distance (5 mm) above the coral tissue after Fo stabilized. Two random spots on either side of a single fragment were measured to obtain average measures of Fv/Fm. All readings with Fo values that were less than 110 were removed to avoid any false detections (Marzonie et al., 2022). The following morning at 07:00 corals were photographed with a color standard (WDKK Waterproof Color Chart, DGK Color Tools) to assess the effect of temperature on coral color, a proxy for relative chlorophyll density and bleaching severity(Winters et al. 2009; Voolstra et al. 2020).&amp;amp;nbsp;&amp;lt;/p&amp;gt;

&amp;lt;p&amp;gt;Image analysis of coral color, a proxy for bleaching severity&amp;lt;/p&amp;gt;

&amp;lt;p&amp;gt;Coral color was determined from each photograph in a semi-automated manner. Each photograph was first cropped to a standard size to remove excess background via a custom automated batch script in Adobe Photoshop (Version 21.1.2). Photographs were then loaded into ImageJ (v1.53c (Schneider et al. 2012) ), and the performance of 16 built-in segmentation models were tested on a sub-sample of coral images to remove the background of the cropped image, which was turned to black, thus leaving only the coral fragment. The segmentation model that best segmented all coral fragments from the background effectively with limited coral fragment cut off (Model Li) was then implemented on all images, which were batch processed using a custom image segmentation macro script modified from(Strock 2021). Once segmented, the script then extracted red pixel intensity of the fragment in RGB, HSB, and LAB color spaces. Finally, the mean red pixel intensity of the red color standard from the original (unsegmented) images was extracted from a region of interest drawn by hand in ImageJ. Pixel intensities of the coral and corresponding red standard were then converted to a ‘darkness’ score by subtracting the red channel 'brightness’ from the maximum value (255). The mean red channel darkness of each coral was then normalized by dividing by the mean red pixel darkness of the red color standard from the same photograph. These red-normalized color values were then used to calculate the changes in bleaching severity between species, sites and treatments. For visualization, the red-normalized color values were divided by the mean color under ambient (MMM) conditions for that species.&amp;lt;br /&amp;gt;
&amp;lt;br /&amp;gt;
&amp;lt;strong&amp;gt;Organism identifiers (Genus, Lifesciences Identifier [LSID]):&amp;lt;/strong&amp;gt;&amp;lt;br /&amp;gt;
Pocillopora,&amp;amp;nbsp;urn:lsid:marinespecies.org:taxname:206938&amp;lt;br /&amp;gt;
Porites,&amp;amp;nbsp;urn:lsid:marinespecies.org:taxname:206485&amp;lt;br /&amp;gt;
Acropora,&amp;amp;nbsp;urn:lsid:marinespecies.org:taxname:205469&amp;lt;/p&amp;gt;</gco:CharacterString>
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        <gmx:Anchor xlink:href="http://lod.bco-dmo.org/id/award/843346.rdf" xlink:title="OCE-1923743" xlink:actuate="onRequest">Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1923743 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1923743</gmx:Anchor>
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http://lod.bco-dmo.org/id/dataset-parameter/935303.rdf
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	Name: Temperature
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http://lod.bco-dmo.org/id/dataset-parameter/935310.rdf
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http://lod.bco-dmo.org/id/dataset-parameter/935311.rdf
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http://lod.bco-dmo.org/id/dataset-parameter/935312.rdf
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http://lod.bco-dmo.org/id/dataset-parameter/935313.rdf
	Name: Label
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http://lod.bco-dmo.org/id/dataset-parameter/935316.rdf
	Name: Name
	Units: unitless
	Description: &lt;p&gt;updated filename with color channel information added as a suffix _RGB_## (see Supplemental Files for images within Heron_STHS_photos.zip)&lt;/p&gt; 
http://lod.bco-dmo.org/id/dataset-parameter/935317.rdf
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http://lod.bco-dmo.org/id/dataset-parameter/935318.rdf
	Name: Mean_frag
	Units: unitless
	Description: &lt;p&gt;mean pixel intensity across the coral fragment&lt;/p&gt; 
http://lod.bco-dmo.org/id/dataset-parameter/935319.rdf
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http://lod.bco-dmo.org/id/dataset-parameter/935320.rdf
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http://lod.bco-dmo.org/id/dataset-parameter/935321.rdf
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http://lod.bco-dmo.org/id/dataset-parameter/935322.rdf
	Name: MaxThr1
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http://lod.bco-dmo.org/id/dataset-parameter/935323.rdf
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                <gco:CharacterString>&amp;lt;p&amp;gt;Acute heat stress experiment&amp;lt;/p&amp;gt;

&amp;lt;p&amp;gt;A standardized temperature profile was used to measure heat tolerance in corals (e.g., (Voolstra et al. 2020; Cunning et al. 2021; Marzonie et al. 2022; Evensen et al. 2023)) with minor modification in temperature profiles. The climatological maximum monthly mean (MMM) of Heron Reef is 27.3°C (Weeks et al. 2008). A pilot experiment with all three genera indicated no difference in Fv/Fm between MMM, MMM+3°C and MMM+6°C, so the latter two treatments were increased to more accurately assess the decline in performance, such that the five treatments used here included ambient, MMM, MMM+4°C, MMM+6.5°C, and MMM+9°C. Generally, experiments began at ~12:00 with a 3-hr ramp to respective treatment temperatures (23°C, 27.3°C, 31.3°C, 33.8°C, 36.3°C), a 3-hr hold, and a 1-hr ramp down to MMM (Evensen et al. 2023) (Figure S1&amp;amp;nbsp;of&amp;amp;nbsp;Brown et al., 2024). Lights were turned off at the onset of the 1-hr ramp down to correspond with sunset. Due to experimental constraints (space, equipment, and time), only two treatments (n = 1 tank) were performed per day and each site was done in isolation. Accordingly, a complete assay took two days per site, with treatments tested each day selected randomly (Table S1, Figure S1&amp;amp;nbsp;of Brown et al., 2024). A fragment from each coral colony was randomly placed into each treatment, so that all colonies were present in each treatment. Temperatures were controlled using an Apex controller (Neptune Systems). Apex temperature probes were calibrated against a high-precision temperature probe (HANNA HI-98190; accuracy: ±0.4°C at 25°C; resolution: ± 0.10°C) at the onset of the experiment. Temperatures were also recorded using cross-calibrated temperature loggers (HOBO UA-001-64, accuracy: ± 0.29°C at 25°C). Photosynthetically active radiation (PAR) was static and controlled using aquarium lights (NICREW HyperReef LED, Shenzhen NiCai Technology Co.), averaging 250 µmol m-2 sec-1.&amp;amp;nbsp;&amp;lt;/p&amp;gt;

&amp;lt;p&amp;gt;Physiological responses to acute heat stress&amp;lt;/p&amp;gt;

&amp;lt;p&amp;gt;At the end of the ramp and after 1 h of darkness (~19:00), corals were assessed for dark-adapted photochemical yield (Fv/Fm) using a Diving-PAM (Walz GmbH) 5-mm diameter fiber-optic probe at a standardized distance (5 mm) above the coral tissue after Fo stabilized. Two random spots on either side of a single fragment were measured to obtain average measures of Fv/Fm. All readings with Fo values that were less than 110 were removed to avoid any false detections (Marzonie et al., 2022). The following morning at 07:00 corals were photographed with a color standard (WDKK Waterproof Color Chart, DGK Color Tools) to assess the effect of temperature on coral color, a proxy for relative chlorophyll density and bleaching severity(Winters et al. 2009; Voolstra et al. 2020).&amp;amp;nbsp;&amp;lt;/p&amp;gt;

&amp;lt;p&amp;gt;Image analysis of coral color, a proxy for bleaching severity&amp;lt;/p&amp;gt;

&amp;lt;p&amp;gt;Coral color was determined from each photograph in a semi-automated manner. Each photograph was first cropped to a standard size to remove excess background via a custom automated batch script in Adobe Photoshop (Version 21.1.2). Photographs were then loaded into ImageJ (v1.53c (Schneider et al. 2012) ), and the performance of 16 built-in segmentation models were tested on a sub-sample of coral images to remove the background of the cropped image, which was turned to black, thus leaving only the coral fragment. The segmentation model that best segmented all coral fragments from the background effectively with limited coral fragment cut off (Model Li) was then implemented on all images, which were batch processed using a custom image segmentation macro script modified from(Strock 2021). Once segmented, the script then extracted red pixel intensity of the fragment in RGB, HSB, and LAB color spaces. Finally, the mean red pixel intensity of the red color standard from the original (unsegmented) images was extracted from a region of interest drawn by hand in ImageJ. Pixel intensities of the coral and corresponding red standard were then converted to a ‘darkness’ score by subtracting the red channel 'brightness’ from the maximum value (255). The mean red channel darkness of each coral was then normalized by dividing by the mean red pixel darkness of the red color standard from the same photograph. These red-normalized color values were then used to calculate the changes in bleaching severity between species, sites and treatments. For visualization, the red-normalized color values were divided by the mean color under ambient (MMM) conditions for that species.&amp;lt;br /&amp;gt;
&amp;lt;br /&amp;gt;
&amp;lt;strong&amp;gt;Organism identifiers (Genus, Lifesciences Identifier [LSID]):&amp;lt;/strong&amp;gt;&amp;lt;br /&amp;gt;
Pocillopora,&amp;amp;nbsp;urn:lsid:marinespecies.org:taxname:206938&amp;lt;br /&amp;gt;
Porites,&amp;amp;nbsp;urn:lsid:marinespecies.org:taxname:206485&amp;lt;br /&amp;gt;
Acropora,&amp;amp;nbsp;urn:lsid:marinespecies.org:taxname:205469&amp;lt;/p&amp;gt;</gco:CharacterString>
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                <gco:CharacterString>&amp;lt;p&amp;gt;For more detailed information on analysis and results,&amp;amp;nbsp;please see: Brown, et al. (2024).&amp;lt;/p&amp;gt;</gco:CharacterString>
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                  <gco:CharacterString>* Tables imported into BCO-DMO data system from provided files &amp;quot;All sites yield data.csv&amp;quot; and &amp;quot;Color scores all HB2.csv.
* After discussion with data submitter, color score data was joined into the all sites yield table using the colonyID as a key(colony id, treatment). 
** Missing data values are displayed differently based on the file format you download.  They are blank in csv files, &amp;quot;NaN&amp;quot; in MatLab files, etc.

* 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]

* file &amp;quot;ed50_revised.csv&amp;quot; renamed &amp;quot;ed50.csv&amp;quot; and attached to dataset as supplemental file.

* Site list with site name, site code, lat, lon was provided by email and joined into the data tables for this dataset. 

* Submitter clarified that there are no images of ambient treatment corals since they were not imaged.</gco:CharacterString>
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            <gco:CharacterString>PI Supplied Instrument Name:  PI Supplied Instrument Description:photochemical yield (Fv/Fm): Diving-PAM (Walz GmbH) Instrument Name: Fluorometer Instrument Short Name:Fluorometer   Instrument Description: A fluorometer or fluorimeter is a device used to measure parameters of fluorescence: its intensity and wavelength distribution of emission spectrum after excitation by a certain spectrum of light. The instrument is designed to measure the amount of stimulated electromagnetic radiation produced by pulses of electromagnetic radiation emitted into a water sample or in situ. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/113/</gco:CharacterString>
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        </gmi:MI_Instrument>
      </gmi:instrument>
      <gmi:instrument>
        <gmi:MI_Instrument>
          <gmi:identifier>
            <gmd:MD_Identifier>
              <gmd:code>
                <gmx:Anchor xlink:href="http://lod.bco-dmo.org/id/instrument/784686.rdf" xlink:title="Onset HOBO Pendant Temperature/Light Data Logger" xlink:actuate="onRequest">temperature loggers (HOBO UA-001-64)</gmx:Anchor>
              </gmd:code>
            </gmd:MD_Identifier>
          </gmi:identifier>
          <gmi:type>
            <gco:CharacterString>temperature loggers (HOBO UA-001-64)</gco:CharacterString>
          </gmi:type>
          <gmi:description>
            <gco:CharacterString>PI Supplied Instrument Name: temperature loggers (HOBO UA-001-64) PI Supplied Instrument Description:Temperatures were controlled using an Apex controller (Neptune Systems). Apex temperature probes were calibrated against a high-precision temperature probe (HANNA HI-98190; accuracy: ±0.4°C at 25°C; resolution: ± 0.10°C) at the onset of the experiment. Temperatures were also recorded using cross-calibrated temperature loggers (HOBO UA-001-64, accuracy: ± 0.29°C at 25°C). Instrument Name: Onset HOBO Pendant Temperature/Light Data Logger Instrument Short Name:Onset HOBO Pendant Temp/Light   Instrument Description: The Onset HOBO (model numbers UA-002-64 or UA-001-64) is an in-situ instrument for wet or underwater applications. It supports light intensity, soil temperature, temperature, and water temperature. A two-channel logger with 10-bit resolution can record up to approximately 28,000 combined temperature and light measurements with 64K bytes memory. It has a polypropylene housing case. Uses an optical USB to transmit data. A solar radiation shield is used for measurement in sunlight. Temperature measurement range: -20 deg C to 70 deg C (temperature). Light measurement range: 0 to 320,000 lux. Temperature accuracy: +/- 0.53 deg C from 0 deg C to 50 deg C. Light accuracy: Designed for measurement of relative light levels. Water depth rating: 30 m.</gco:CharacterString>
          </gmi:description>
        </gmi:MI_Instrument>
      </gmi:instrument>
      </gmi:MI_AcquisitionInformation>
  </gmi:acquisitionInformation>
</gmi:MI_Metadata>
