Table 1.

Evaluation results on the CryoPPP test dataset. The EMPIAR ID of the cryo-EM image set for each of the seven test proteins is listed in column 1. The type of each protein, number of cryo-EM images and number of labeled particles are reported in columns 2–4. The precision, recall, F1-score and Dice score are reported in the other columns. Bold font denotes the best average score of each metric

EMPIAR ID	Type of protein	Num. of labeled images	Num. of labeled particles	Metrics	Template-based	Deep Picker	CrYOLO	Topaz	CASSPER	CryoTransformer	CryoSegNet
10028 [34]	Ribosome (80S)	300	26,391	Precision	0.845	0.848	0.807	0.696	0.877	0.751	0.833
				Recall	0.935	0.920	0.941	0.937	0.591	0.832	0.944
				F1-Score	0.888	0.883	0.869	0.799	0.706	0.789	0.885
				Dice Score	0.872	0.861	0.863	0.786	0.668	0.826	0.859
10081 [35]	Transport	300	39,352	Precision	0.853	0.868	0.822	0.732	0.915	0.860	0.835
				Recall	0.900	0.900	0.884	0.872	0.796	0.889	0.922
				F1-Score	0.876	0.883	0.852	0.796	0.851	0.874	0.876
				Dice Score	0.877	0.822	0.822	0.758	0.834	0.823	0.876
10345 [36]	Signaling	295	15,894	Precision	0.743	0.912	0.648	0.544	0.598	0.744	0.746
				Recall	0.924	0.504	0.665	0.805	0.716	0.864	0.920
				F1-Score	0.824	0.649	0.656	0.650	0.652	0.799	0.824
				Dice Score	0.707	0.578	0.452	0.507	0.532	0.684	0.743
11056 [37]	Transport	305	125,908	Precision	0.717	0.717	0.726	0.764	0.768	0.853	0.757
				Recall	0.306	0.306	0.780	0.909	0.292	0.683	0.687
				F1-Score	0.429	0.429	0.752	0.830	0.423	0.758	0.720
				Dice Score	0.401	0.401	0.718	0.778	0.398	0.679	0.663
10532 [38]	Viral	300	87,933	Precision	0.790	0.621	0.756	0.732	0.848	0.813	0.796
				Recall	0.716	0.682	0.774	0.939	0.385	0.665	0.628
				F1-Score	0.751	0.650	0.765	0.823	0.530	0.732	0.702
				Dice Score	0.743	0.432	0.724	0.788	0.519	0.614	0.649
10093 [39]	Membrane	295	56,394	Precision	0.672	0.756	0.623	0.610	0.632	0.560	0.716
				Recall	0.613	0.349	0.744	0.216	0.596	0.689	0.515
				F1-Score	0.641	0.478	0.678	0.319	0.613	0.618	0.600
				Dice Score	0.568	0.437	0.641	0.279	0.513	0.600	0.537
10017 [40]	β-Galactosidase	84	49,391	Precision	0.814	0.795	0.824	0.847	0.860	0.745	0.859
				Recall	0.822	0.691	0.588	0.936	0.770	0.587	0.616
				F1-Score	0.818	0.739	0.686	0.889	0.813	0.657	0.718
				Dice Score	0.813	0.764	0.663	0.886	0.808	0.623	0.703
Average				Precision	0.776	0.788	0.744	0.704	0.785	0.761	0.792
				Recall	0.745	0.622	0.768	0.802	0.592	0.744	0.747
				F1-Score	0.747	0.673	0.751	0.729	0.655	0.747	0.761
				Dice Score	0.712	0.614	0.698	0.683	0.610	0.693	0.719