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Table 2 The segmentation efficacy (shown as Dice coefficient) of individual segmentation steps on raw and reconstructed image data

From: Cell segmentation methods for label-free contrast microscopy: review and comprehensive comparison

Method Segmentation efficacy (Dice coefficient)
  QPI DIC HMC PC
  raw raw rDIC Koos [12] rDIC Yin [13] raw rDIC Koos [12] rDIC Yin [13] raw rPC Yin [14] rPC TopHat [15]
Foreground-background segmentation
 sWekaGraphCut 0.96 0.86 0.89 0.84 0.86 0.84 0.84 0.86 0.80 0.84
 sIllastikGraphCut 0.94 0.87 0.89 0.84 0.87 0.84 0.84 0.80 0.80 0.84
 sWeka 0.94 0.85 0.87 0.80 0.85 0.82 0.79 0.81 0.72 0.81
 sIlastik 0.94 0.85 0.86 0.80 0.82 0.82 0.79 0.84 0.72 0.82
 sLS-Caselles 0.88 0.83 0.82 0.79 0.84 0.79 0.79 0.77 0.75 0.79
 sEGT 0.89 0.88 0.85 0.64 0.86 0.79 0.70 0.74 0.68 0.79
 sPC-Phantast N/A N/A N/A N/A N/A N/A N/A 0.77 N/A N/A
 sPC-Juneau 0.85 0.85 0.84 0.59 0.82 0.77 0.69 0.73 0.72 0.76
 sPC-Topman N/A N/A N/A N/A N/A N/A N/A 0.72 N/A N/A
 sLS-ChanVese 0.61 0.48 0.74 0.55 0.68 0.67 0.36 0.64 0.65 0.76
 sGraphCut 0.92 0.38 0.78 0.64 0.32 0.59 0.58 0.40 0.70 0.74
 sST 0.92 0.339 0.76 0.61 0.31 0.72 0.53 0.40 0.69 0.73
 sPT 0.83 0.34 0.60 0.34 0.30 0.46 0.08 0.29 0.67 0.73
 sOtsu 0.62 0.34 0.36 0.31 0.28 0.16 0.18 0.24 0.51 0.66
Cell detection (seed point extraction)
 dGRST 0.94 0.65 0.79 0.85 0.75 0.81 0.85 0.81 0.77 0.88
 dLoGm-Kong 0.90 0.83 0.90 0.86 0.72 0.84 0.85 0.52 0.69 0.78
 dFRST 0.94 0.58 0.78 0.82 0.70 0.78 0.82 0.82 0.74 0.88
 dLoGm-Peng 0.89 0.71 0.86 0.78 0.69 0.83 0.86 0.51 0.73 0.84
 dLoGg-Kong 0.85 0.83 0.80 0.84 0.74 0.82 0.83 0.43 0.72 0.79
 dDT-Weka 0.81 0.68 0.81 0.74 0.73 0.72 0.75 0.80 0.76 0.78
 dLoGg-Xu 0.84 0.77 0.80 0.80 0.65 0.81 0.78 0.52 0.71 0.78
 dDT-Threshold 0.94 0.26 0.91 0.86 0.54 0.86 0.84 0.49 0.76 0.81
 dRV-Qi 0.77 0.61 0.57 0.58 0.70 0.48 0.48 0.82 0.59 0.65
 dMSER 0.93 0.06 0.55 0.58 0.29 0.82 0.69 0.65 0.79 0.68
 dCellDetect 0.92 0.00 0.88 0.89 0.00 0.83 0.84 0.00 0.71 0.81
 dLoGh-Zhang 0.82 0.13 0.52 0.64 0.25 0.63 0.65 0.49 0.70 0.61
Single cell (instance) segmentation
 MCWS-dDT 0.77 0.58 0.66 0.61 0.47 0.54 0.55 0.52 0.37 0.62
 MCWS 0.82 0.55 0.69 0.63 0.26 0.54 0.53 0.41 0.39 0.60
 aioFogbank 0.71 0.54 0.55 0.42 0.44 0.38 0.39 0.46 0.34 0.19
 aioCellProfiler 0.69 0.37 0.55 0.38 0.19 0.45 0.27 0.09 0.41 0.54
 aioDMGW 0.82 0.08 0.62 0.38 0.00 0.48 0.29 0.10 0.39 0.65
 aioFasright 0.21 0.15 0.43 0.00 0.00 0.26 0.14 0.03 0.37 0.57
 aioCellX 0.34 0.03 0.08 0.21 0.02 0.18 0.05 0.07 0.03 0.16
 aioFastER 0.09 0.03 0.07 0.00 0.02 0.17 0.01 0.25 0.08 0.06
  1. Sorted by Dice coefficient (high to low). N/A, not applicable, for foreground background segmentation, methods designated for PC image were not deployed on other microscopic modalities