Supplementary data - raw unprocessed images, segmentation ground truth and image reconstructions. 

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abbreviations
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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


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folder structure and file and filename description
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folder "source data+groundtruth"
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- 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"
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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.