June 5, 2024 Dataset Open Access

De, Trina; Urbanski, Adrian; Thangamani, Subasini; Wyrzykowska, Maria; Yakimovich, Artur

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="024" ind1=" " ind2=" ">
    <subfield code="a">10.14278/rodare.3001</subfield>
    <subfield code="2">doi</subfield>
  </datafield>
  <controlfield tag="005">20240606080315.0</controlfield>
  <controlfield tag="001">3001</controlfield>
  <datafield tag="100" ind1=" " ind2=" ">
    <subfield code="a">De, Trina</subfield>
    <subfield code="u">Center for Advanced Systems Understanding, Helmholtz-Zentrum Dresden-Rossendorf</subfield>
    <subfield code="0">(orcid)0000-0003-1111-9851</subfield>
  </datafield>
  <datafield tag="245" ind1=" " ind2=" ">
    <subfield code="a">HeLaCytoNuc: fluorescence microscopy dataset with segmentation masks for cell nuclei and cytoplasm</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="260" ind1=" " ind2=" ">
    <subfield code="c">2024-06-05</subfield>
  </datafield>
  <datafield tag="980" ind1=" " ind2=" ">
    <subfield code="a">dataset</subfield>
  </datafield>
  <datafield tag="650" ind1="1" ind2="7">
    <subfield code="a">cc-by</subfield>
    <subfield code="2">opendefinition.org</subfield>
  </datafield>
  <datafield tag="773" ind1=" " ind2=" ">
    <subfield code="a">https://www.hzdr.de/publications/Publ-39181</subfield>
    <subfield code="i">isIdenticalTo</subfield>
    <subfield code="n">url</subfield>
  </datafield>
  <datafield tag="773" ind1=" " ind2=" ">
    <subfield code="a">10.14278/rodare.3000</subfield>
    <subfield code="i">isVersionOf</subfield>
    <subfield code="n">doi</subfield>
  </datafield>
  <datafield tag="909" ind1="C" ind2="O">
    <subfield code="o">oai:rodare.hzdr.de:3001</subfield>
    <subfield code="p">openaire_data</subfield>
    <subfield code="p">user-health</subfield>
    <subfield code="p">user-rodare</subfield>
  </datafield>
  <datafield tag="980" ind1=" " ind2=" ">
    <subfield code="a">user-health</subfield>
  </datafield>
  <datafield tag="980" ind1=" " ind2=" ">
    <subfield code="a">user-rodare</subfield>
  </datafield>
  <datafield tag="700" ind1=" " ind2=" ">
    <subfield code="a">Urbanski, Adrian</subfield>
    <subfield code="u">Center for Advanced Systems Understanding, Helmholtz-Zentrum Dresden-Rossendorf</subfield>
    <subfield code="0">(orcid)0009-0008-6619-3665</subfield>
  </datafield>
  <datafield tag="700" ind1=" " ind2=" ">
    <subfield code="a">Thangamani, Subasini</subfield>
    <subfield code="u">Center for Advanced Systems Understanding, Helmholtz-Zentrum Dresden-Rossendorf</subfield>
  </datafield>
  <datafield tag="700" ind1=" " ind2=" ">
    <subfield code="a">Wyrzykowska, Maria</subfield>
    <subfield code="u">Center for Advanced Systems Understanding, Helmholtz-Zentrum Dresden-Rossendorf</subfield>
  </datafield>
  <datafield tag="700" ind1=" " ind2=" ">
    <subfield code="a">Yakimovich, Artur</subfield>
    <subfield code="u">Center for Advanced Systems Understanding, Helmholtz-Zentrum Dresden-Rossendorf</subfield>
    <subfield code="0">(orcid)0000-0003-2458-4904</subfield>
  </datafield>
  <datafield tag="542" ind1=" " ind2=" ">
    <subfield code="l">open</subfield>
  </datafield>
  <datafield tag="856" ind1="4" ind2=" ">
    <subfield code="s">8595625573</subfield>
    <subfield code="u">https://rodare.hzdr.de/record/3001/files/HeLaCytoNuc_raw_images.zip</subfield>
    <subfield code="z">md5:8d00f9b3bbcd8653d12439dc797ba497</subfield>
  </datafield>
  <datafield tag="856" ind1="4" ind2=" ">
    <subfield code="s">3666113</subfield>
    <subfield code="u">https://rodare.hzdr.de/record/3001/files/HeLaCytoNuc_test_cellprofiler_masks.zip</subfield>
    <subfield code="z">md5:7324a5d360fef7dacd6d625384aadc4a</subfield>
  </datafield>
  <datafield tag="856" ind1="4" ind2=" ">
    <subfield code="s">76153291</subfield>
    <subfield code="u">https://rodare.hzdr.de/record/3001/files/HeLaCytoNuc_test.zip</subfield>
    <subfield code="z">md5:de45497da77317486f6ed51224a8e3d5</subfield>
  </datafield>
  <datafield tag="856" ind1="4" ind2=" ">
    <subfield code="s">434887789</subfield>
    <subfield code="u">https://rodare.hzdr.de/record/3001/files/HeLaCytoNuc_train.zip</subfield>
    <subfield code="z">md5:ca89238d7be977939ca0a67b94306891</subfield>
  </datafield>
  <datafield tag="856" ind1="4" ind2=" ">
    <subfield code="s">139881304</subfield>
    <subfield code="u">https://rodare.hzdr.de/record/3001/files/HeLaCytoNuc_validation.zip</subfield>
    <subfield code="z">md5:bb684299f81dfb2e12f47ae8e5bbfbcd</subfield>
  </datafield>
  <datafield tag="041" ind1=" " ind2=" ">
    <subfield code="a">eng</subfield>
  </datafield>
  <datafield tag="653" ind1=" " ind2=" ">
    <subfield code="a">Fluorescence microscopy</subfield>
  </datafield>
  <datafield tag="653" ind1=" " ind2=" ">
    <subfield code="a">high content microscopy</subfield>
  </datafield>
  <datafield tag="653" ind1=" " ind2=" ">
    <subfield code="a">cytoskeleton</subfield>
  </datafield>
  <datafield tag="653" ind1=" " ind2=" ">
    <subfield code="a">cell nuclei</subfield>
  </datafield>
  <datafield tag="520" ind1=" " ind2=" ">
    <subfield code="a">&lt;p&gt;&lt;strong&gt;Data Description:&lt;/strong&gt;&lt;/p&gt;

&lt;p&gt;This dataset comprises fluorescence micrographs of HeLa cells, specifically labelled to identify nuclei and cell cytoplasm. These images were acquired as a technical calibration for a high-content screening study detailed and published in [1].&lt;/p&gt;

&lt;p&gt;The HeLa cell line (ATCC-CCL-2), a widely used immortalised cell line in laboratory research, was cultured under standard conditions. Post-cultivation, the cells were fixed and stained with fluorescent dyes to visualise the nuclei and cytoplasm. The nuclei were stained with DAPI (4&amp;#39;,6-diamidino-2-phenylindole), a blue-fluorescent DNA stain, while fluorescent-labeled phalloidin was used to detect actin filaments and delineate the cytoplasm. The entire process of cell culture, fixation, staining, and imaging adhered strictly to the protocols described in [1].&lt;/p&gt;

&lt;p&gt;The preprocessed dataset includes 2,676 8-bit RGB images, each with a pixel resolution of 520 x 696 pixels. In these images, only two of the RGB channels are utilized: the red channel represents the cytoplasm, and the blue channel represents the nuclei. The dataset is divided into training, validation, and test subsets in a 70:20:10 ratio. The entire dataset is accompanied by instance segmentation masks for nuclei and cytoplasm objects obtained through a specialised CellProfiler [2] software. Notably, the test subset was annotated manually by a specialist, ensuring high-quality annotations. The original raw images are of a higher resolution, 1040 x 1392 pixels, and have a bit depth of 16 bits, providing more detailed information for advanced analyses.&lt;/p&gt;

&lt;p&gt;&lt;br&gt;
&lt;strong&gt;File&amp;nbsp;Description:&lt;/strong&gt;&lt;/p&gt;

&lt;p&gt;The file structure of the zip files is as follows:&lt;/p&gt;



&lt;p&gt;HeLaCytoNuc_{train/validation/test}.zip -&amp;gt;&lt;/p&gt;

&lt;p&gt;- images -&amp;gt; {filename}.tif&lt;/p&gt;

&lt;p&gt;- nuclei_masks&amp;nbsp; -&amp;gt; {filename}.tif&lt;/p&gt;

&lt;p&gt;- cytoplasm_masks&amp;nbsp; -&amp;gt; {filename}.tif&lt;/p&gt;



&lt;p&gt;HeLaCytoNuc_raw_images.zip -&amp;gt; {filename}.tif&lt;/p&gt;



&lt;p&gt;HeLaCytoNuc_test_cellprofiler_masks.zip -&amp;gt;&lt;/p&gt;

&lt;p&gt;- nuclei_masks&amp;nbsp; -&amp;gt; {filename}.tif&lt;/p&gt;

&lt;p&gt;- cytoplasm_masks&amp;nbsp; -&amp;gt; {filename}.tif&amp;nbsp;&lt;/p&gt;



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

&lt;p&gt;1.&amp;nbsp;R&amp;auml;m&amp;ouml;, Pauli, Anna Drewek, C&amp;eacute;cile Arrieumerlou, Niko Beerenwinkel, Houchaima Ben-Tekaya, Bettina Cardel, Alain Casanova et al. &amp;quot;Simultaneous analysis of large-scale RNAi screens for pathogen entry.&amp;quot;&amp;nbsp;&lt;em&gt;BMC genomics&lt;/em&gt;&amp;nbsp;15 (2014): 1-18.&lt;/p&gt;

&lt;p&gt;2.&amp;nbsp;Carpenter, Anne E., Thouis R. Jones, Michael R. Lamprecht, Colin Clarke, In Han Kang, Ola Friman, David A. Guertin et al. &amp;quot;CellProfiler: image analysis software for identifying and quantifying cell phenotypes.&amp;quot;&amp;nbsp;&lt;em&gt;Genome biology&lt;/em&gt;&amp;nbsp;7 (2006): 1-11.&lt;/p&gt;</subfield>
  </datafield>
</record>