The most relevant features of colony morphology and textures determined by Fisher scores using training data (40) were involved in the classification of the iPSC colony quality. On the basis of the Fisher scores, the features with the lowest score were not considered as the most relevant for quality estimation in this study. The Fisher score of each feature of colony morphology and textures for discriminating the quality is presented in S2 and S3 Tables, respectively. Only features that had a Fisher score higher than a certain threshold (e.g., 0.450) were kept, whereas others that showed a less discriminant effect on the classifier were removed. Under the colony morphology feature, the equivalent diameter, minor axis, major axis, solidity, and extent were selected as being the most relevant features, showing higher Fisher scores than the other features. Under textures, the sum variance, variance, sum entropy, entropy, sum average, and information measures of correlation_2 were selected as the most relevant features. The ranges of values of these features for the healthy colonies were higher than those for the unhealthy colonies are depicted in Fig 6. The potential of each individual morphological and textural feature in distinguishing the iPSC colonies was examined from the area under the curve (AUC), using receiver operating characteristic curve analysis (NCSS 11 Statistical Software, Kaysville, UT, USA). The performance of each individual morphological and textural feature (estimated through AUC values) in distinguishing the colonies is summarized in Table 1. Among the morphological features, solidity outperformed the rest with an AUC value of 0.878 ± 0.03 and a confidence interval (CI) of 0.747–0.933 (Fig 7). Among the textures, variance (AUC = 0.859 ± 0.03, CI = 0.741–0.926) slightly outperformed the sum entropy and sum variance in distinguishing the colonies (Fig 8).