Application of high-throughput phenotyping tool Tomato Analyzer to characterize Balkan Capsicum fruit diversity

•To the best of our knowledge, this is second report on Tomato Analyzer (TA) application for fruit diversity examination of Balkan pepper collection.•Five varietal types of elongated, round, conical, bell or blocky, and pumpkin shape were established based on fruit shape visual assessment.•Relatedness of fruit descriptors measured by conventional descriptors and TA displayed that respective fruit traits were measured differently and were neither substitutable nor repetitive.•Correlation network suggest that fruit size, homogeneity, and color were tightly linked whereas fruit blockiness, asymmetry, and pericarp thickness were not linked.•It is anticipated that this research will assist pepper breeders to better understand pepper fruit diversity to develop pepper varieties with desirable fruit shape.