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    <title>lopc</title>
    <link rel="alternate" type="text/html" href="http://www.seascapemodeling.org/lopc/" />
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    <id>tag:www.seascapemodeling.org,2010-07-07:/lopc//5</id>
    <updated>2010-08-16T19:55:53Z</updated>
    <subtitle>A blog for the community of laser optical plankton counter users</subtitle>
    <generator uri="http://www.sixapart.com/movabletype/">Movable Type 4.23-en</generator>

<entry>
    <title>Ctenophores?</title>
    <link rel="alternate" type="text/html" href="http://www.seascapemodeling.org/lopc/2010/08/ctenophores.html" />
    <id>tag:www.seascapemodeling.org,2010:/lopc//5.138</id>

    <published>2010-08-16T19:51:24Z</published>
    <updated>2010-08-16T19:55:53Z</updated>

    <summary><![CDATA[Andy's image of a ctenophore is nice, and it makes me want to snorkel.&nbsp; But instead, I'm here at work--so here I am, snorkeling through a mass of LOPC data.&nbsp; And what do I find?&nbsp; Something that looks a lot...]]></summary>
    <author>
        <name>Nick Record</name>
        
    </author>
    
    <category term="ctenophore" label="ctenophore" scheme="http://www.sixapart.com/ns/types#tag" />
    <category term="lopc" label="lopc" scheme="http://www.sixapart.com/ns/types#tag" />
    
    <content type="html" xml:lang="en-us" xml:base="http://www.seascapemodeling.org/lopc/">
        <![CDATA[Andy's <a href="http://www.seascapemodeling.org/seascape_projects/2010/08/ctenophore.html">image of a ctenophore</a> is nice, and it makes me want to snorkel.&nbsp; But instead, I'm here at work--so here I am, snorkeling through a mass of LOPC data.&nbsp; And what do I find?&nbsp; Something that looks a lot like it might be a bunch of ctenophores!<br /><br />Of course, there's no way to be sure.&nbsp; But it looks compelling.<br /><br /><span class="mt-enclosure mt-enclosure-image" style="display: inline;"><a href="http://www.seascapemodeling.org/lopc/ctenophores.jpg"><img alt="ctenophores.jpg" src="http://www.seascapemodeling.org/lopc/assets_c/2010/08/ctenophores-thumb-420x354-473.jpg" class="mt-image-none" style="" height="354" width="420" /></a></span><br /> <div><br /></div>]]>
        
    </content>
</entry>

<entry>
    <title>What do lasered copepods look like?</title>
    <link rel="alternate" type="text/html" href="http://www.seascapemodeling.org/lopc/2010/08/what-do-lasered-copepods-look-like.html" />
    <id>tag:www.seascapemodeling.org,2010:/lopc//5.135</id>

    <published>2010-08-12T17:49:55Z</published>
    <updated>2010-08-12T18:16:00Z</updated>

    <summary><![CDATA[I've whittled down the huge collection of laser-profiled shapes to a small collection that are almost certainly mostly copepods--in particular, finmarks (Calanus finmarchicus).&nbsp; My almost-certainty is based on an anomalously large aggregation at just the depth and size range where...]]></summary>
    <author>
        <name>Nick Record</name>
        
    </author>
    
    <category term="copepod" label="copepod" scheme="http://www.sixapart.com/ns/types#tag" />
    <category term="forwardproblem" label="forward problem" scheme="http://www.sixapart.com/ns/types#tag" />
    <category term="laseropticalplanktoncounter" label="laser optical plankton counter" scheme="http://www.sixapart.com/ns/types#tag" />
    <category term="lopc" label="LOPC" scheme="http://www.sixapart.com/ns/types#tag" />
    <category term="mep" label="mep" scheme="http://www.sixapart.com/ns/types#tag" />
    
    <content type="html" xml:lang="en-us" xml:base="http://www.seascapemodeling.org/lopc/">
        <![CDATA[I've whittled down the huge collection of laser-profiled shapes to a small collection that are almost certainly mostly copepods--in particular, finmarks (Calanus finmarchicus).&nbsp; My almost-certainty is based on an anomalously large aggregation at just the depth and size range where we'd expect finmarks to be found.&nbsp; The problem is that they are tiny compared to the resolution of the LOPC, and I would like to convince myself that the blobs I'm seeing really are finmarks.<br /><br />Here's what the blobs look like in the LOPC data.<br /><br /><span class="mt-enclosure mt-enclosure-image" style="display: inline;"><a href="http://www.seascapemodeling.org/lopc/WilkiFins.jpg"><img alt="WilkiFins.jpg" src="http://www.seascapemodeling.org/lopc/assets_c/2010/08/WilkiFins-thumb-420x394-456.jpg" class="mt-image-none" style="" height="394" width="420" /></a></span><br /> <div><br />There is no way to tell by looking at these (I would argue), that they are copepods, let alone finmarks.&nbsp; (A few of them are probably something else entirely.)&nbsp; In order to help convince myself that these blob shapes are really what I think they are, I've written a script that solves the "forward problem"--i.e. estimating what a copepod would look like if it passed through the laser.&nbsp; I'm sure I'm not the first to have done this, but it only took a few minutes, and it looks pretty neat.<br /><br />Here's the copepod I start with.<br /><span class="mt-enclosure mt-enclosure-image" style="display: inline;"><a href="http://www.seascapemodeling.org/lopc/cop2mep01.jpg"><img alt="cop2mep01.jpg" src="http://www.seascapemodeling.org/lopc/assets_c/2010/08/cop2mep01-thumb-420x315-458.jpg" class="mt-image-none" style="" height="315" width="420" /></a></span><br />Step one is to outline the shape that passes through the LOPC:<br /><br /><span class="mt-enclosure mt-enclosure-image" style="display: inline;"><a href="http://www.seascapemodeling.org/lopc/cop2mep02.jpg"><img alt="cop2mep02.jpg" src="http://www.seascapemodeling.org/lopc/assets_c/2010/08/cop2mep02-thumb-420x315-460.jpg" class="mt-image-none" style="" height="315" width="420" /></a></span><br /><br />Next I transform the image to binary.&nbsp; This disregards the differing levels of transparency of the animal, but I'm just going for an approximation here, so I'm okay with that.<br /><br /><span class="mt-enclosure mt-enclosure-image" style="display: inline;"><a href="http://www.seascapemodeling.org/lopc/cop2mep03.jpg"><img alt="cop2mep03.jpg" src="http://www.seascapemodeling.org/lopc/assets_c/2010/08/cop2mep03-thumb-420x315-462.jpg" class="mt-image-none" style="" height="315" width="420" /></a></span><br /><br />Finally I pass it through an imaginary LOPC.&nbsp; The amount of dark pixels within the imaginary beam determines the strength of the return.&nbsp; I also use a threshold of about 5% pixel cover.&nbsp; This is what it looks like:<br /><br /><span class="mt-enclosure mt-enclosure-image" style="display: inline;"><a href="http://www.seascapemodeling.org/lopc/cop2mep04.jpg"><img alt="cop2mep04.jpg" src="http://www.seascapemodeling.org/lopc/assets_c/2010/08/cop2mep04-thumb-420x315-464.jpg" class="mt-image-none" style="" height="315" width="420" /></a></span><br /><br />It actually coheres rather nicely with the quasi-silhouettes shown in the first image.&nbsp; Yes, I'm starting to believe, despite the blobular shapes, that these actually are copepods.&nbsp; The next step is to pass the copepod through at different orientations.<br /></div><div><br /></div>]]>
        
    </content>
</entry>

<entry>
    <title>Test shapes from Wilkinson Basin</title>
    <link rel="alternate" type="text/html" href="http://www.seascapemodeling.org/lopc/2010/08/test-shapes-from-wilkinson-basin.html" />
    <id>tag:www.seascapemodeling.org,2010:/lopc//5.134</id>

    <published>2010-08-09T18:41:06Z</published>
    <updated>2010-08-09T18:54:27Z</updated>

    <summary><![CDATA[Pete recently asked me (here) what some of the larger shapes near the surface of Wilkinson Basin are, that show up in the LOPC data.&nbsp; I'm working on some matlab scripts for processing and visualizing the LOPC data, so here's...]]></summary>
    <author>
        <name>Nick Record</name>
        
    </author>
    
    <category term="shapes" label="shapes" scheme="http://www.sixapart.com/ns/types#tag" />
    <category term="wilkinsonbasin" label="Wilkinson Basin" scheme="http://www.sixapart.com/ns/types#tag" />
    
    <content type="html" xml:lang="en-us" xml:base="http://www.seascapemodeling.org/lopc/">
        <![CDATA[Pete recently asked me (<a href="http://www.seascapemodeling.org/seascape_projects/2010/08/the-twilight-series-part-1-diapausers-in-wilkinson-basin.html#comment-60">here</a>) what some of the larger shapes near the surface of Wilkinson Basin are, that show up in the LOPC data.&nbsp; I'm working on some matlab scripts for processing and visualizing the LOPC data, so here's a chance to stretch my dogs.<br /><br />I've grouped the shapes into four size classes (3-4mm, 4-5mm, 5-6mm, and &gt;6 mm) in the four plots below.&nbsp; I'm still working on the y-axis, so at this point, it doesn't represent depth or anything.&nbsp; The x-axis is reliable.<br /><br />The shading of the shapes essentially shows transparency.&nbsp; For example, we'd expect gelatinous plankton to allow more light through their bodies than crustaceans would.&nbsp; It's interesting that there seems to be more transparency for the middle sizes than for the larger or smaller.&nbsp; I'm having a hard time guessing at what these creatures might be, but hopefully some net data will help with that.&nbsp; I won't start to speculate just yet.<br /><br /><span class="mt-enclosure mt-enclosure-image" style="display: inline;"><a href="http://www.seascapemodeling.org/lopc/WilkiShapes3000.jpg"><img alt="WilkiShapes3000.jpg" src="http://www.seascapemodeling.org/lopc/assets_c/2010/08/WilkiShapes3000-thumb-420x597-448.jpg" class="mt-image-none" style="" height="597" width="420" /></a></span><br /><div><br /><span class="mt-enclosure mt-enclosure-image" style="display: inline;"><a href="http://www.seascapemodeling.org/lopc/WilkiShapes4000.jpg"><img alt="WilkiShapes4000.jpg" src="http://www.seascapemodeling.org/lopc/assets_c/2010/08/WilkiShapes4000-thumb-420x783-450.jpg" class="mt-image-none" style="" height="783" width="420" /></a></span><br /><span class="mt-enclosure mt-enclosure-image" style="display: inline;"><a href="http://www.seascapemodeling.org/lopc/WilkiShapes5000.jpg"><img alt="WilkiShapes5000.jpg" src="http://www.seascapemodeling.org/lopc/assets_c/2010/08/WilkiShapes5000-thumb-420x324-452.jpg" class="mt-image-none" style="" height="324" width="420" /></a></span><br /><span class="mt-enclosure mt-enclosure-image" style="display: inline;"><a href="http://www.seascapemodeling.org/lopc/WilkiShapes6000.jpg"><img alt="WilkiShapes6000.jpg" src="http://www.seascapemodeling.org/lopc/assets_c/2010/08/WilkiShapes6000-thumb-420x429-454.jpg" class="mt-image-none" style="" height="429" width="420" /></a></span><br /></div><div><br /></div>]]>
        
    </content>
</entry>

<entry>
    <title>Welcome</title>
    <link rel="alternate" type="text/html" href="http://www.seascapemodeling.org/lopc/2010/07/welcome.html" />
    <id>tag:www.seascapemodeling.org,2010:/lopc//5.122</id>

    <published>2010-07-07T17:35:05Z</published>
    <updated>2010-07-07T17:38:52Z</updated>

    <summary><![CDATA[I'm starting a blog on my work with the LOPC (laser optical plankton counter).&nbsp; I hope to share ideas on using this equipment and analyzing the data that it collects.&nbsp; Those who are interested in contributing can contact me....]]></summary>
    <author>
        <name>Nick Record</name>
        
    </author>
    
    <category term="welcome" label="welcome" scheme="http://www.sixapart.com/ns/types#tag" />
    
    <content type="html" xml:lang="en-us" xml:base="http://www.seascapemodeling.org/lopc/">
        <![CDATA[I'm starting a blog on my work with the LOPC (laser optical plankton counter).&nbsp; I hope to share ideas on using this equipment and analyzing the data that it collects.&nbsp; Those who are interested in contributing can <a href="http://www.umaine.edu/marine/people/directory.php/profile/nicholas_record">contact me</a>. ]]>
        
    </content>
</entry>

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