June 5, 2024 Dataset Open Access

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

Dublin Core Export

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<oai_dc:dc xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:oai_dc="http://www.openarchives.org/OAI/2.0/oai_dc/" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.openarchives.org/OAI/2.0/oai_dc/ http://www.openarchives.org/OAI/2.0/oai_dc.xsd">
  <dc:creator>De, Trina</dc:creator>
  <dc:creator>Urbanski, Adrian</dc:creator>
  <dc:creator>Thangamani, Subasini</dc:creator>
  <dc:creator>Wyrzykowska, Maria</dc:creator>
  <dc:creator>Yakimovich, Artur</dc:creator>
  <dc:date>2024-06-05</dc:date>
  <dc:description>Data Description:

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].

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',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].

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.


File Description:

The file structure of the zip files is as follows:



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

- images -&gt; {filename}.tif

- nuclei_masks  -&gt; {filename}.tif

- cytoplasm_masks  -&gt; {filename}.tif



HeLaCytoNuc_raw_images.zip -&gt; {filename}.tif



HeLaCytoNuc_test_cellprofiler_masks.zip -&gt;

- nuclei_masks  -&gt; {filename}.tif

- cytoplasm_masks  -&gt; {filename}.tif 



References:

1. Rämö, Pauli, Anna Drewek, Cécile Arrieumerlou, Niko Beerenwinkel, Houchaima Ben-Tekaya, Bettina Cardel, Alain Casanova et al. "Simultaneous analysis of large-scale RNAi screens for pathogen entry." BMC genomics 15 (2014): 1-18.

2. Carpenter, Anne E., Thouis R. Jones, Michael R. Lamprecht, Colin Clarke, In Han Kang, Ola Friman, David A. Guertin et al. "CellProfiler: image analysis software for identifying and quantifying cell phenotypes." Genome biology 7 (2006): 1-11.</dc:description>
  <dc:identifier>https://rodare.hzdr.de/record/3001</dc:identifier>
  <dc:identifier>10.14278/rodare.3001</dc:identifier>
  <dc:identifier>oai:rodare.hzdr.de:3001</dc:identifier>
  <dc:language>eng</dc:language>
  <dc:relation>url:https://www.hzdr.de/publications/Publ-39181</dc:relation>
  <dc:relation>doi:10.14278/rodare.3000</dc:relation>
  <dc:relation>url:https://rodare.hzdr.de/communities/health</dc:relation>
  <dc:relation>url:https://rodare.hzdr.de/communities/rodare</dc:relation>
  <dc:rights>info:eu-repo/semantics/openAccess</dc:rights>
  <dc:rights>https://creativecommons.org/licenses/by/4.0/legalcode</dc:rights>
  <dc:subject>Fluorescence microscopy</dc:subject>
  <dc:subject>high content microscopy</dc:subject>
  <dc:subject>cytoskeleton</dc:subject>
  <dc:subject>cell nuclei</dc:subject>
  <dc:title>HeLaCytoNuc: fluorescence microscopy dataset with segmentation masks for cell nuclei and cytoplasm</dc:title>
  <dc:type>info:eu-repo/semantics/other</dc:type>
  <dc:type>dataset</dc:type>
</oai_dc:dc>