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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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{
  "description": "<p>This data set contains confocal stacks from <em>Arabidopsis thaliana </em><em>35S::GFP-MBD</em> 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)</p>\n\n<p>&nbsp;</p>\n\n<p><strong>Material and methods:</strong></p>\n\n<p>Plant material and growth conditions</p>\n\n<p><em>Arabidopsis thaliana </em>wild type Col-0 and the microtubule reporter line <em>GFP-MBD</em> (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&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.</p>\n\n<p>&nbsp;</p>\n\n<p>Confocal microscopy</p>\n\n<p>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 &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&ndash;650 nm. GFP excitation was performed using a 488 nm solid-state laser and fluorescence was detected at 495&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 &mu;m.</p>\n\n<p>&nbsp;</p>\n\n<p><strong>File list:</strong></p>\n\n<p>Light grown hypocotyl, <em>GFP-MBD</em> reporter line:</p>\n\n<p>- Hypocotyl_GFP-MBD.tif</p>\n\n<p>Cotyledon&rsquo;s pavement cells, PI staining:</p>\n\n<p>- PC_PI_Col0_1.tif</p>\n\n<p>- PC_PI_Col0_2.tif</p>\n\n<p>- PC_PI_Col0_3.tif</p>\n\n<p>- PC_PI_Col0_4.tif</p>\n\n<p>- PC_PI_Col0_5.tif</p>\n\n<p>- PC_PI_Col0_6.tif</p>\n\n<p>- PC_PI_Col0_7.tif</p>\n\n<p>- PC_PI_Col0_8.tif</p>\n\n<p>Shoot apical meristem, PI staining:</p>\n\n<p>- SAM_PI_Col-0.tif</p>\n\n<p>&nbsp;</p>\n\n<p><strong>Reference:</strong></p>\n\n<p>Marc, Jan, Cheryl L. Granger, Jennifer Brincat, Deborah D. Fisher, Teh-hui Kao, Andrew G. McCubbin, and Richard J. Cyr. 1998. &ldquo;A GFP&ndash;MAP4 Reporter Gene for Visualizing Cortical Microtubule Rearrangements in Living Epidermal Cells.&rdquo; <em>The Plant Cell</em> 10 (11): 1927&ndash;39. https://doi.org/10.1105/tpc.10.11.1927.</p>", 
  "license": "https://creativecommons.org/licenses/by/4.0/legalcode", 
  "creator": [
    {
      "affiliation": "RDP ENS-Lyon/INRA", 
      "@id": "https://orcid.org/0000-0002-6873-9341", 
      "@type": "Person", 
      "name": "Erguvan \u00d6zer"
    }, 
    {
      "affiliation": "RDP ENS-Lyon/INRA", 
      "@id": "https://orcid.org/0000-0003-3643-3978", 
      "@type": "Person", 
      "name": "Verger St\u00e9phane"
    }
  ], 
  "url": "https://zenodo.org/record/2577053", 
  "datePublished": "2019-02-25", 
  "keywords": [
    "confocal microscopy", 
    "Plants", 
    "Arabidopsis thaliana", 
    "Hypocotyl", 
    "Shoot apical meristem", 
    "Cotyledon pavement cells", 
    "GFP-MBD", 
    "propidium iodide", 
    "SurfCut"
  ], 
  "@context": "https://schema.org/", 
  "distribution": [
    {
      "contentUrl": "https://zenodo.org/api/files/f73d257e-a5ab-46fd-ab62-71cf4c050143/Data.zip", 
      "encodingFormat": "zip", 
      "@type": "DataDownload"
    }
  ], 
  "identifier": "https://doi.org/10.5281/zenodo.2577053", 
  "@id": "https://doi.org/10.5281/zenodo.2577053", 
  "@type": "Dataset", 
  "name": "Dataset of confocal microscopy stacks from plant samples - ImageJ SurfCut: a user-friendly, high-throughput pipeline for extracting cell contours from 3D confocal stacks"
}
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