Dataset Open Access

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


MARC21 XML Export

<?xml version='1.0' encoding='UTF-8'?>
<record xmlns="http://www.loc.gov/MARC21/slim">
  <leader>00000nmm##2200000uu#4500</leader>
  <datafield tag="653" ind1=" " ind2=" ">
    <subfield code="a">confocal microscopy</subfield>
  </datafield>
  <datafield tag="653" ind1=" " ind2=" ">
    <subfield code="a">Plants</subfield>
  </datafield>
  <datafield tag="653" ind1=" " ind2=" ">
    <subfield code="a">Arabidopsis thaliana</subfield>
  </datafield>
  <datafield tag="653" ind1=" " ind2=" ">
    <subfield code="a">Hypocotyl</subfield>
  </datafield>
  <datafield tag="653" ind1=" " ind2=" ">
    <subfield code="a">Shoot apical meristem</subfield>
  </datafield>
  <datafield tag="653" ind1=" " ind2=" ">
    <subfield code="a">Cotyledon pavement cells</subfield>
  </datafield>
  <datafield tag="653" ind1=" " ind2=" ">
    <subfield code="a">GFP-MBD</subfield>
  </datafield>
  <datafield tag="653" ind1=" " ind2=" ">
    <subfield code="a">propidium iodide</subfield>
  </datafield>
  <datafield tag="653" ind1=" " ind2=" ">
    <subfield code="a">SurfCut</subfield>
  </datafield>
  <controlfield tag="005">20200124192611.0</controlfield>
  <controlfield tag="001">2577053</controlfield>
  <datafield tag="700" ind1=" " ind2=" ">
    <subfield code="u">RDP ENS-Lyon/INRA</subfield>
    <subfield code="0">(orcid)0000-0003-3643-3978</subfield>
    <subfield code="a">Verger Stéphane</subfield>
  </datafield>
  <datafield tag="856" ind1="4" ind2=" ">
    <subfield code="s">535863808</subfield>
    <subfield code="z">md5:a0b132b74d0c772115472b84caa6566e</subfield>
    <subfield code="u">https://zenodo.org/record/2577053/files/Data.zip</subfield>
  </datafield>
  <datafield tag="542" ind1=" " ind2=" ">
    <subfield code="l">open</subfield>
  </datafield>
  <datafield tag="260" ind1=" " ind2=" ">
    <subfield code="c">2019-02-25</subfield>
  </datafield>
  <datafield tag="909" ind1="C" ind2="O">
    <subfield code="p">openaire_data</subfield>
    <subfield code="o">oai:zenodo.org:2577053</subfield>
  </datafield>
  <datafield tag="100" ind1=" " ind2=" ">
    <subfield code="u">RDP ENS-Lyon/INRA</subfield>
    <subfield code="0">(orcid)0000-0002-6873-9341</subfield>
    <subfield code="a">Erguvan Özer</subfield>
  </datafield>
  <datafield tag="245" ind1=" " ind2=" ">
    <subfield code="a">Dataset of confocal microscopy stacks from plant samples - ImageJ SurfCut: a user-friendly, high-throughput pipeline for extracting cell contours from 3D confocal stacks</subfield>
  </datafield>
  <datafield tag="536" ind1=" " ind2=" ">
    <subfield code="c">615739</subfield>
    <subfield code="a">Mechanical signals in plants: from cellular mechanisms to growth coordination and patterning</subfield>
  </datafield>
  <datafield tag="540" ind1=" " ind2=" ">
    <subfield code="u">https://creativecommons.org/licenses/by/4.0/legalcode</subfield>
    <subfield code="a">Creative Commons Attribution 4.0 International</subfield>
  </datafield>
  <datafield tag="650" ind1="1" ind2="7">
    <subfield code="a">cc-by</subfield>
    <subfield code="2">opendefinition.org</subfield>
  </datafield>
  <datafield tag="520" ind1=" " ind2=" ">
    <subfield code="a">&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;</subfield>
  </datafield>
  <datafield tag="773" ind1=" " ind2=" ">
    <subfield code="n">doi</subfield>
    <subfield code="i">isVersionOf</subfield>
    <subfield code="a">10.5281/zenodo.2577052</subfield>
  </datafield>
  <datafield tag="024" ind1=" " ind2=" ">
    <subfield code="a">10.5281/zenodo.2577053</subfield>
    <subfield code="2">doi</subfield>
  </datafield>
  <datafield tag="980" ind1=" " ind2=" ">
    <subfield code="a">dataset</subfield>
  </datafield>
</record>
620
128
views
downloads
All versions This version
Views 620620
Downloads 128128
Data volume 68.6 GB68.6 GB
Unique views 498498
Unique downloads 107107

Share

Cite as