Dataset Open Access
De, Trina; Urbanski, Adrian; Thangamani, Subasini; Wyrzykowska, Maria; Yakimovich, Artur
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rdf:about="https://doi.org/10.14278/rodare.3001"> <rdf:type rdf:resource="http://www.w3.org/ns/dcat#Dataset"/> <dct:type rdf:resource="http://purl.org/dc/dcmitype/Dataset"/> <dct:identifier rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">https://doi.org/10.14278/rodare.3001</dct:identifier> <foaf:page rdf:resource="https://doi.org/10.14278/rodare.3001"/> <dct:creator> <rdf:Description rdf:about="http://orcid.org/0000-0003-1111-9851"> <rdf:type rdf:resource="http://xmlns.com/foaf/0.1/Agent"/> <foaf:name>De, Trina</foaf:name> <foaf:givenName>Trina</foaf:givenName> <foaf:familyName>De</foaf:familyName> <org:memberOf> <foaf:Organization> <foaf:name>Center for Advanced Systems Understanding, Helmholtz-Zentrum Dresden-Rossendorf</foaf:name> </foaf:Organization> </org:memberOf> </rdf:Description> </dct:creator> <dct:creator> <rdf:Description rdf:about="http://orcid.org/0009-0008-6619-3665"> <rdf:type rdf:resource="http://xmlns.com/foaf/0.1/Agent"/> <foaf:name>Urbanski, Adrian</foaf:name> <foaf:givenName>Adrian</foaf:givenName> <foaf:familyName>Urbanski</foaf:familyName> <org:memberOf> <foaf:Organization> <foaf:name>Center for Advanced Systems Understanding, Helmholtz-Zentrum Dresden-Rossendorf</foaf:name> </foaf:Organization> </org:memberOf> </rdf:Description> </dct:creator> <dct:creator> <rdf:Description> <rdf:type rdf:resource="http://xmlns.com/foaf/0.1/Agent"/> <foaf:name>Thangamani, Subasini</foaf:name> <foaf:givenName>Subasini</foaf:givenName> <foaf:familyName>Thangamani</foaf:familyName> <org:memberOf> <foaf:Organization> <foaf:name>Center for Advanced Systems Understanding, Helmholtz-Zentrum Dresden-Rossendorf</foaf:name> </foaf:Organization> </org:memberOf> </rdf:Description> </dct:creator> <dct:creator> <rdf:Description> <rdf:type rdf:resource="http://xmlns.com/foaf/0.1/Agent"/> <foaf:name>Wyrzykowska, Maria</foaf:name> <foaf:givenName>Maria</foaf:givenName> <foaf:familyName>Wyrzykowska</foaf:familyName> <org:memberOf> <foaf:Organization> <foaf:name>Center for Advanced Systems Understanding, Helmholtz-Zentrum Dresden-Rossendorf</foaf:name> </foaf:Organization> </org:memberOf> </rdf:Description> </dct:creator> <dct:creator> <rdf:Description rdf:about="http://orcid.org/0000-0003-2458-4904"> <rdf:type rdf:resource="http://xmlns.com/foaf/0.1/Agent"/> <foaf:name>Yakimovich, Artur</foaf:name> <foaf:givenName>Artur</foaf:givenName> <foaf:familyName>Yakimovich</foaf:familyName> <org:memberOf> <foaf:Organization> <foaf:name>Center for Advanced Systems Understanding, Helmholtz-Zentrum Dresden-Rossendorf</foaf:name> </foaf:Organization> </org:memberOf> </rdf:Description> </dct:creator> <dct:title>HeLaCytoNuc: fluorescence microscopy dataset with segmentation masks for cell nuclei and cytoplasm</dct:title> <dct:publisher> <foaf:Agent> <foaf:name>Rodare</foaf:name> </foaf:Agent> </dct:publisher> <dct:issued rdf:datatype="http://www.w3.org/2001/XMLSchema#gYear">2024</dct:issued> <dcat:keyword>Fluorescence microscopy</dcat:keyword> <dcat:keyword>high content microscopy</dcat:keyword> <dcat:keyword>cytoskeleton</dcat:keyword> <dcat:keyword>cell nuclei</dcat:keyword> <dct:issued rdf:datatype="http://www.w3.org/2001/XMLSchema#date">2024-06-05</dct:issued> <dct:language rdf:resource="http://publications.europa.eu/resource/authority/language/ENG"/> <owl:sameAs rdf:resource="https://rodare.hzdr.de/record/3001"/> <adms:identifier> <adms:Identifier> <skos:notation rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">https://rodare.hzdr.de/record/3001</skos:notation> </adms:Identifier> </adms:identifier> <owl:sameAs rdf:resource="https://www.hzdr.de/publications/Publ-39181"/> <dct:isVersionOf rdf:resource="https://doi.org/10.14278/rodare.3000"/> <dct:isPartOf rdf:resource="https://rodare.hzdr.de/communities/health"/> <dct:isPartOf rdf:resource="https://rodare.hzdr.de/communities/rodare"/> <owl:versionInfo>Version 1</owl:versionInfo> <dct:description><p><strong>Data Description:</strong></p> <p>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].</p> <p>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&#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].</p> <p>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.</p> <p><br> <strong>File&nbsp;Description:</strong></p> <p>The file structure of the zip files is as follows:</p> <p>HeLaCytoNuc_{train/validation/test}.zip -&gt;</p> <p>- images -&gt; {filename}.tif</p> <p>- nuclei_masks&nbsp; -&gt; {filename}.tif</p> <p>- cytoplasm_masks&nbsp; -&gt; {filename}.tif</p> <p>HeLaCytoNuc_raw_images.zip -&gt; {filename}.tif</p> <p>HeLaCytoNuc_test_cellprofiler_masks.zip -&gt;</p> <p>- nuclei_masks&nbsp; -&gt; {filename}.tif</p> <p>- cytoplasm_masks&nbsp; -&gt; {filename}.tif&nbsp;</p> <p><strong>References:</strong></p> <p>1.&nbsp;R&auml;m&ouml;, Pauli, Anna Drewek, C&eacute;cile Arrieumerlou, Niko Beerenwinkel, Houchaima Ben-Tekaya, Bettina Cardel, Alain Casanova et al. &quot;Simultaneous analysis of large-scale RNAi screens for pathogen entry.&quot;&nbsp;<em>BMC genomics</em>&nbsp;15 (2014): 1-18.</p> <p>2.&nbsp;Carpenter, Anne E., Thouis R. Jones, Michael R. Lamprecht, Colin Clarke, In Han Kang, Ola Friman, David A. Guertin et al. &quot;CellProfiler: image analysis software for identifying and quantifying cell phenotypes.&quot;&nbsp;<em>Genome biology</em>&nbsp;7 (2006): 1-11.</p></dct:description> <dct:accessRights rdf:resource="http://publications.europa.eu/resource/authority/access-right/PUBLIC"/> <dct:accessRights> <dct:RightsStatement rdf:about="info:eu-repo/semantics/openAccess"> <rdfs:label>Open Access</rdfs:label> </dct:RightsStatement> </dct:accessRights> <dcat:distribution> <dcat:Distribution> <dct:rights> <dct:RightsStatement rdf:about="https://creativecommons.org/licenses/by/4.0/legalcode"> <rdfs:label>Creative Commons Attribution 4.0 International</rdfs:label> </dct:RightsStatement> </dct:rights> <dcat:accessURL rdf:resource="https://doi.org/10.14278/rodare.3001"/> </dcat:Distribution> </dcat:distribution> </rdf:Description> </rdf:RDF>
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