Comparison and practical review of segmentation approaches for label-free microscopy

• Main Authors: Tomas Vicar, Jan Balvan, Tomas Slaby, Josef Jaros, Florian Jug, Radim Kolar, Michal Masarik, Jaromir Gumulec
• Format: Dataset
• Language: unknown
• Published: 2018
• Subjects: microscopy; cell segmentation; image reconstruction; differential image; quantitative phase imaging; label-free; Olympus; Orca
• Online Access: https://zenodo.org/record/1250729; https://doi.org/10.5281/zenodo.1250729

This dataset contains microscopic images of PNT1A cell line captured by multiple microcopic without use of any 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. See Vicar et al. Cell segmentation methods for label-free contrast microscopy: review and comprehensive comparison. BMC Bioinformatics (2019) 20:360. DOI 10.1186/s12859-019-2880-8 Code using this dataset is available at https://github.com/tomasvicar/Cell-segmentation-methods-comparison Materials and methods Cells were cultured in RPMI-1640 medium supplemented with antibiotics (penicillin 100 U/ml and streptomycin 0.1 mg/ml) with 10% fetal bovine serum. Prior microscopy acquisition, cells were maintained at 37 cenigrade in a humidified incubator with 5% CO2. Intentionally, high passage number of cells was used (>30) in order to describe distinct morphological heterogeneity of cells (rounded and spindle-shaped, relatively small to large polyploid cells). For acquisition purposes, cells were cultivated in Flow chambers µ-Slide I Luer Family (Ibidi, Martinsried, Germany). Quantitative phase imaging (QPI) microscopy was performed on Tescan Q-PHASE (Tescan, Brno, Czech republic), with objective Nikon CFI Plan Fluor 10x/0.30 captured by Ximea MR4021MC (Ximea, Münster, Germany). Imaging is based on the original concept of coherence-controlled holographic microscope \cite{Kolman:10,Slaby:13}, images are shown in grayscale with units of pg/µm2. DIC microscopy was performed on microscope Nikon A1R (Nikon, Tokyo, Japan), with objective Nikon CFI Plan Apo VC 20x/0.75 captured by CCD camera Jenoptik ProgRes MF (Jenoptik, Jena, Germany). HMC microscopy was performed on microscope Olympus IX71 (Olympus, Tokyo, Japan), with objective Olympus CplanFL N 10x/0.3 RC1 captured by CCD camera Hamamatsu Photonics ORCA-R2 (Hamamatsu Photonics K.K., Hamamatsu, Japan). PC microscopy was performed on a Nikon Eclipse ...