June 5, 2024 Dataset Open Access

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

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  <identifier identifierType="DOI">10.14278/rodare.3001</identifier>
  <creators>
    <creator>
      <creatorName>De, Trina</creatorName>
      <givenName>Trina</givenName>
      <familyName>De</familyName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0003-1111-9851</nameIdentifier>
      <affiliation>Center for Advanced Systems Understanding, Helmholtz-Zentrum Dresden-Rossendorf</affiliation>
    </creator>
    <creator>
      <creatorName>Urbanski, Adrian</creatorName>
      <givenName>Adrian</givenName>
      <familyName>Urbanski</familyName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0009-0008-6619-3665</nameIdentifier>
      <affiliation>Center for Advanced Systems Understanding, Helmholtz-Zentrum Dresden-Rossendorf</affiliation>
    </creator>
    <creator>
      <creatorName>Thangamani, Subasini</creatorName>
      <givenName>Subasini</givenName>
      <familyName>Thangamani</familyName>
      <affiliation>Center for Advanced Systems Understanding, Helmholtz-Zentrum Dresden-Rossendorf</affiliation>
    </creator>
    <creator>
      <creatorName>Wyrzykowska, Maria</creatorName>
      <givenName>Maria</givenName>
      <familyName>Wyrzykowska</familyName>
      <affiliation>Center for Advanced Systems Understanding, Helmholtz-Zentrum Dresden-Rossendorf</affiliation>
    </creator>
    <creator>
      <creatorName>Yakimovich, Artur</creatorName>
      <givenName>Artur</givenName>
      <familyName>Yakimovich</familyName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0003-2458-4904</nameIdentifier>
      <affiliation>Center for Advanced Systems Understanding, Helmholtz-Zentrum Dresden-Rossendorf</affiliation>
    </creator>
  </creators>
  <titles>
    <title>HeLaCytoNuc: fluorescence microscopy dataset with segmentation masks for cell nuclei and cytoplasm</title>
  </titles>
  <publisher>Rodare</publisher>
  <publicationYear>2024</publicationYear>
  <subjects>
    <subject>Fluorescence microscopy</subject>
    <subject>high content microscopy</subject>
    <subject>cytoskeleton</subject>
    <subject>cell nuclei</subject>
  </subjects>
  <dates>
    <date dateType="Issued">2024-06-05</date>
  </dates>
  <language>en</language>
  <resourceType resourceTypeGeneral="Dataset"/>
  <alternateIdentifiers>
    <alternateIdentifier alternateIdentifierType="url">https://rodare.hzdr.de/record/3001</alternateIdentifier>
  </alternateIdentifiers>
  <relatedIdentifiers>
    <relatedIdentifier relatedIdentifierType="URL" relationType="IsIdenticalTo">https://www.hzdr.de/publications/Publ-39181</relatedIdentifier>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="IsVersionOf">10.14278/rodare.3000</relatedIdentifier>
    <relatedIdentifier relatedIdentifierType="URL" relationType="IsPartOf">https://rodare.hzdr.de/communities/health</relatedIdentifier>
    <relatedIdentifier relatedIdentifierType="URL" relationType="IsPartOf">https://rodare.hzdr.de/communities/rodare</relatedIdentifier>
  </relatedIdentifiers>
  <version>Version 1</version>
  <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;&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;</description>
  </descriptions>
</resource>