DOI: 10.5281/zenodo.1250729
title: Comparison and practical review of segmentation approaches for label-free microscopy

description: 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 TS100-F microscope, with a Nikon CFI Achro ADL 10x/0.25 objective captured by CCD camera Jenoptik ProgRes MF.


Folder structure and file and filename description

folder "source data+groundtruth"
- includes raw microscopic data 
  (uncompressed 16-bit for DIC, HMC and PC, 32-bit for QPI)
- includes manualy annotated groundtruth (zip file - imageJ ROI file, 1bit png mask)


e.g. 
DIC_01_raw.tif
DIC_01_groundtruth_imagejROI.zip
DIC_01_groundtruth_mask.png



folder "reconstructions"


includes reconstructed images using reconstructions with highest dice coefficient achieved. 


for DIC and HMC: rDIC-Koos, rDIC-Yin, and rWeka
for PC: rPC-Top-Hat, rDIC-Yin, and rWeka
for QPI: rWeka


note that for rWeka images numbered 01 for DIC, HMC and PC and 01-03 for QPI were used for learning.


Abbreviations
DIC, differential image contrast
HMC, Hoffman modulation contrast
PC, phase contrast
QPI, quantitative phase imaging
rDIC-Koos, DIC/HMC image reconstruction according to Koos et al, Sci Rep. 2016;6:30420
rDIC-Yin, DIC/HMC image reconstruction according to Yin et al, Inf Process Med Imaging. 2011;22:384-97.
rPC-Yin, PC image reconstruction according to Yin et al,  Med Im Anal. 2012; 16(5):1047
rPC-Top-Hat, Top-Hat filter according to Dewan et al, IEEE Transactions on Biomedical Circuits and
Systems.2014;8(5):716-728
rWeka, probability map using Trainable Weka segmentation according to Arganda-Carreras et al. Bioinformatics. 2017
description: This work was supported by the Czech Science Foundation GACR 18-24089S