Dataset Open Access
De, Trina; Urbanski, Adrian; Thangamani, Subasini; Wyrzykowska, Maria; Yakimovich, Artur
{ "description": "<p><strong>Data Description:</strong></p>\n\n<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>\n\n<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',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>\n\n<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>\n\n<p><br>\n<strong>File Description:</strong></p>\n\n<p>The file structure of the zip files is as follows:</p>\n\n\n\n<p>HeLaCytoNuc_{train/validation/test}.zip -></p>\n\n<p>- images -> {filename}.tif</p>\n\n<p>- nuclei_masks -> {filename}.tif</p>\n\n<p>- cytoplasm_masks -> {filename}.tif</p>\n\n\n\n<p>HeLaCytoNuc_raw_images.zip -> {filename}.tif</p>\n\n\n\n<p>HeLaCytoNuc_test_cellprofiler_masks.zip -></p>\n\n<p>- nuclei_masks -> {filename}.tif</p>\n\n<p>- cytoplasm_masks -> {filename}.tif </p>\n\n\n\n<p><strong>References:</strong></p>\n\n<p>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." <em>BMC genomics</em> 15 (2014): 1-18.</p>\n\n<p>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." <em>Genome biology</em> 7 (2006): 1-11.</p>", "inLanguage": { "name": "English", "alternateName": "eng", "@type": "Language" }, "url": "https://rodare.hzdr.de/record/3001", "@type": "Dataset", "creator": [ { "name": "De, Trina", "@type": "Person", "@id": "https://orcid.org/0000-0003-1111-9851", "affiliation": "Center for Advanced Systems Understanding, Helmholtz-Zentrum Dresden-Rossendorf" }, { "name": "Urbanski, Adrian", "@type": "Person", "@id": "https://orcid.org/0009-0008-6619-3665", "affiliation": "Center for Advanced Systems Understanding, Helmholtz-Zentrum Dresden-Rossendorf" }, { "name": "Thangamani, Subasini", "@type": "Person", "affiliation": "Center for Advanced Systems Understanding, Helmholtz-Zentrum Dresden-Rossendorf" }, { "name": "Wyrzykowska, Maria", "@type": "Person", "affiliation": "Center for Advanced Systems Understanding, Helmholtz-Zentrum Dresden-Rossendorf" }, { "name": "Yakimovich, Artur", "@type": "Person", "@id": "https://orcid.org/0000-0003-2458-4904", "affiliation": "Center for Advanced Systems Understanding, Helmholtz-Zentrum Dresden-Rossendorf" } ], "keywords": [ "Fluorescence microscopy", "high content microscopy", "cytoskeleton", "cell nuclei" ], "@id": "https://doi.org/10.14278/rodare.3001", "@context": "https://schema.org/", "datePublished": "2024-06-05", "name": "HeLaCytoNuc: fluorescence microscopy dataset with segmentation masks for cell nuclei and cytoplasm", "distribution": [ { "contentUrl": "https://rodare.hzdr.de/api/files/fae71336-c6d2-45b2-ae65-416c8f57b5a0/HeLaCytoNuc_raw_images.zip", "fileFormat": "zip", "@type": "DataDownload" }, { "contentUrl": "https://rodare.hzdr.de/api/files/fae71336-c6d2-45b2-ae65-416c8f57b5a0/HeLaCytoNuc_test_cellprofiler_masks.zip", "fileFormat": "zip", "@type": "DataDownload" }, { "contentUrl": "https://rodare.hzdr.de/api/files/fae71336-c6d2-45b2-ae65-416c8f57b5a0/HeLaCytoNuc_test.zip", "fileFormat": "zip", "@type": "DataDownload" }, { "contentUrl": "https://rodare.hzdr.de/api/files/fae71336-c6d2-45b2-ae65-416c8f57b5a0/HeLaCytoNuc_train.zip", "fileFormat": "zip", "@type": "DataDownload" }, { "contentUrl": "https://rodare.hzdr.de/api/files/fae71336-c6d2-45b2-ae65-416c8f57b5a0/HeLaCytoNuc_validation.zip", "fileFormat": "zip", "@type": "DataDownload" } ], "sameAs": [ "https://www.hzdr.de/publications/Publ-39181" ], "version": "Version 1", "license": "https://creativecommons.org/licenses/by/4.0/legalcode", "identifier": "https://doi.org/10.14278/rodare.3001" }
All versions | This version | |
---|---|---|
Views | 217 | 217 |
Downloads | 76 | 76 |
Data volume | 122.4 GB | 122.4 GB |
Unique views | 187 | 187 |
Unique downloads | 50 | 50 |