This dataset contains microscopic images of multiple cell lines captured by quantitative phase microscopy (QPI) without use of any fluorescent labeling and a manually annotated ground truth for subsequent use in segmentation algorithms. Dataset also includes images reconstructed according to the methods described below in order to ease further segmentation. Our data consist of quantitative phase microscopy images: 244 labelled images of PC-3 (7,907 cells), 205 labelled PNT1A (9,288 cells), 25 labelled images of G361, 25 labelled images of A2050 and 25 labelled images of HOB cells , in the paper designated as "labelled", and 1,819 unlabelled images with a mixture of 22Rv1, A2058, A2780, DU145, Fadu, G361, HOB and LNCaP used for pretraining, in the paper designated as "unlabelled". See Vicar et al. XXXX 2021 DOI XXX (TBA after publishing) Code using this dataset is available at github.com/tomasvicar/Deep-QPI-Cell-Segmentation Materials and methods A set of adherent cell lines of various origins, tumorigenic potential, and morphology were used in this paper (PC-3, PNT1A, 22Rv1, DU145, LNCaP, A2058, A2780, Fadu, G361, HOB). PC-3, PNT1A, 22Rv1, DU145, LNCaP, A2780, and G361 cell lines were cultured in RPMI-1640 medium, A2058, FaDu, and HOB cell lines were cultured in DMEM-F12 medium, all supplemented with antibiotics (penicillin 100 U/ml and streptomycin 0.1 mg/ml), and with 10% fetal bovine serum (FBS). Prior to microscopy acquisition, the cells were maintained at 37 °C in a humidified (60%) incubator with 5% CO\textsubscript{2} (Sanyo, Japan). For acquisition purposes, the cells were cultivated in the Flow chamber µ-Slide I Luer Family (Ibidi, Martinsried, Germany). To maintain standard cultivation conditions during time-lapse experiments, cells were placed in the gas chamber H201 - for Mad City Labs Z100/Z500 piezo Z-stage (Okolab, Ottaviano NA, Italy). For the acquisition of QPI, a coherence-controlled holographic microscope (Telight, Q-Phase) was used. Objective Nikon Plan 10×/0.3 was used for hologram acquisition with a CCD camera (XIMEA MR4021MC). Holographic data were numerically reconstructed with the Fourier transform method (described in Slaby, 2013 and phase unwrapping was used on the phase image. QPI datasets used in this paper were acquired during various experimental setups and treatments. In most cases, experiments were conducted with the time-lapse acquisition. The final dataset contains images acquired at least three hours apart. Folder structure and file and filename description labelled (labelled): cells with segmentation labels, e.g. 00001_PC3_img.tif - 32bit tiff image (in pg/um2 values) 00001_PC3_mask.png - 8bit image with mask with unique grayscale value corresponding to single cell in FOV. unlabelled (unlabelled): 11 varying cell lines, total 1819 FOVs, 32bit tiff image (in pg/um2 values)

This work is supported by the Czech Science Foundation, project no. 18-24089S.