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

Vicar, Tomas; Balvan, Jan; Jaros, Josef; Jug, Florian; Kolar, Radim; Masarik, Michal; Gumulec, Jaromir

doi:10.1186/s12859-019-2880-8

BMC Bioinformatics

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

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

Back to article page

ISSN: 1471-2105

Contact us

General enquiries: journalsubmissions@springernature.com