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Dataset of confocal microscopy stacks from plant samples - ImageJ SurfCut: a user-friendly, high-throughput pipeline for extracting cell contours from 3D confocal stacks

Erguvan Özer; Verger Stéphane


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  <identifier identifierType="DOI">10.5281/zenodo.2577053</identifier>
  <creators>
    <creator>
      <creatorName>Erguvan Özer</creatorName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0002-6873-9341</nameIdentifier>
      <affiliation>RDP ENS-Lyon/INRA</affiliation>
    </creator>
    <creator>
      <creatorName>Verger Stéphane</creatorName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0003-3643-3978</nameIdentifier>
      <affiliation>RDP ENS-Lyon/INRA</affiliation>
    </creator>
  </creators>
  <titles>
    <title>Dataset of confocal microscopy stacks from plant samples - ImageJ SurfCut: a user-friendly, high-throughput pipeline for extracting cell contours from 3D confocal stacks</title>
  </titles>
  <publisher>Zenodo</publisher>
  <publicationYear>2019</publicationYear>
  <subjects>
    <subject>confocal microscopy</subject>
    <subject>Plants</subject>
    <subject>Arabidopsis thaliana</subject>
    <subject>Hypocotyl</subject>
    <subject>Shoot apical meristem</subject>
    <subject>Cotyledon pavement cells</subject>
    <subject>GFP-MBD</subject>
    <subject>propidium iodide</subject>
    <subject>SurfCut</subject>
  </subjects>
  <dates>
    <date dateType="Issued">2019-02-25</date>
  </dates>
  <resourceType resourceTypeGeneral="Dataset"/>
  <alternateIdentifiers>
    <alternateIdentifier alternateIdentifierType="url">https://zenodo.org/record/2577053</alternateIdentifier>
  </alternateIdentifiers>
  <relatedIdentifiers>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="IsVersionOf">10.5281/zenodo.2577052</relatedIdentifier>
  </relatedIdentifiers>
  <rightsList>
    <rights rightsURI="https://creativecommons.org/licenses/by/4.0/legalcode">Creative Commons Attribution 4.0 International</rights>
    <rights rightsURI="info:eu-repo/semantics/openAccess">Open Access</rights>
  </rightsList>
  <descriptions>
    <description descriptionType="Abstract">&lt;p&gt;This data set contains confocal stacks from &lt;em&gt;Arabidopsis thaliana &lt;/em&gt;&lt;em&gt;35S::GFP-MBD&lt;/em&gt; light grown hypocotyl as well as propidium iodide stained cotyledon pavement cells and shoot apical meristem. This is the test dataset for the Fiji macro SurfCut (https://github.com/sverger/SurfCut; 10.5281/zenodo.2635737)&lt;/p&gt;

&lt;p&gt;&amp;nbsp;&lt;/p&gt;

&lt;p&gt;&lt;strong&gt;Material and methods:&lt;/strong&gt;&lt;/p&gt;

&lt;p&gt;Plant material and growth conditions&lt;/p&gt;

&lt;p&gt;&lt;em&gt;Arabidopsis thaliana &lt;/em&gt;wild type Col-0 and the microtubule reporter line &lt;em&gt;GFP-MBD&lt;/em&gt; (WS-4, (Marc et al. 1998) were used. Seeds were cold treated for 48 hr to synchronize germination. Plants were then grown in a phytotron at 20&amp;deg;C, in a 16 hr light/8 hr dark cycle on solid Murashige and Skoog medium (MS medium, Duchefa, Haarlem, the Netherlands) with 0.8% agar, 1% sucrose, and no vitamin.&lt;/p&gt;

&lt;p&gt;&amp;nbsp;&lt;/p&gt;

&lt;p&gt;Confocal microscopy&lt;/p&gt;

&lt;p&gt;Cell contour staining in the case of PC_PI_Col0_(1-8).tif and SAM_PI_Col-0.tif was performed by staining the cell wall with Propidium Iodide (PI). Plants were immersed in 0.2 mg/ml propidium iodide (PI, Sigma-Aldrich) for 10 min and washed with water prior to imaging. For imaging, samples were either placed on a solid agar medium and immersed in water, or placed between glass slide and coverslip separated by 400 &amp;mu;m spacers to prevent tissue crushing. Images were acquired using a Leica TCS SP8 confocal microscope, equipped with a water immersion objective (HCX IRAPO L 25x/0.95 W). PI excitation was performed using a 552 nm solid-state laser and fluorescence was detected at 600&amp;ndash;650 nm. GFP excitation was performed using a 488 nm solid-state laser and fluorescence was detected at 495&amp;ndash;535 nm. Stacks of 1024x1024 pixels (pixel size of 0.363 x 0.363 micron) optical section were generated with a Z interval of 0.5 &amp;mu;m.&lt;/p&gt;

&lt;p&gt;&amp;nbsp;&lt;/p&gt;

&lt;p&gt;&lt;strong&gt;File list:&lt;/strong&gt;&lt;/p&gt;

&lt;p&gt;Light grown hypocotyl, &lt;em&gt;GFP-MBD&lt;/em&gt; reporter line:&lt;/p&gt;

&lt;p&gt;- Hypocotyl_GFP-MBD.tif&lt;/p&gt;

&lt;p&gt;Cotyledon&amp;rsquo;s pavement cells, PI staining:&lt;/p&gt;

&lt;p&gt;- PC_PI_Col0_1.tif&lt;/p&gt;

&lt;p&gt;- PC_PI_Col0_2.tif&lt;/p&gt;

&lt;p&gt;- PC_PI_Col0_3.tif&lt;/p&gt;

&lt;p&gt;- PC_PI_Col0_4.tif&lt;/p&gt;

&lt;p&gt;- PC_PI_Col0_5.tif&lt;/p&gt;

&lt;p&gt;- PC_PI_Col0_6.tif&lt;/p&gt;

&lt;p&gt;- PC_PI_Col0_7.tif&lt;/p&gt;

&lt;p&gt;- PC_PI_Col0_8.tif&lt;/p&gt;

&lt;p&gt;Shoot apical meristem, PI staining:&lt;/p&gt;

&lt;p&gt;- SAM_PI_Col-0.tif&lt;/p&gt;

&lt;p&gt;&amp;nbsp;&lt;/p&gt;

&lt;p&gt;&lt;strong&gt;Reference:&lt;/strong&gt;&lt;/p&gt;

&lt;p&gt;Marc, Jan, Cheryl L. Granger, Jennifer Brincat, Deborah D. Fisher, Teh-hui Kao, Andrew G. McCubbin, and Richard J. Cyr. 1998. &amp;ldquo;A GFP&amp;ndash;MAP4 Reporter Gene for Visualizing Cortical Microtubule Rearrangements in Living Epidermal Cells.&amp;rdquo; &lt;em&gt;The Plant Cell&lt;/em&gt; 10 (11): 1927&amp;ndash;39. https://doi.org/10.1105/tpc.10.11.1927.&lt;/p&gt;</description>
  </descriptions>
  <fundingReferences>
    <fundingReference>
      <funderName>European Commission</funderName>
      <funderIdentifier funderIdentifierType="Crossref Funder ID">10.13039/501100000780</funderIdentifier>
      <awardNumber awardURI="info:eu-repo/grantAgreement/EC/FP7/615739/">615739</awardNumber>
      <awardTitle>Mechanical signals in plants: from cellular mechanisms to growth coordination and patterning</awardTitle>
    </fundingReference>
  </fundingReferences>
</resource>
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