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Semantic segmentation has been proposed as a tool to accelerate the processing of natural history collection images. However, developing a flexible and resilient segmentation network requires an approach for adaptation which allows processing different datasets with minimal training and validation. This paper presents a cross-validation approach designed to determine whether a semantic segmentation network possesses the flexibility required for application across different collections and institutions. Consequently, the specific objectives of cross-validating the semantic segmentation network are to (a) evaluate the effectiveness of the network for segmenting image sets derived from collections different from the one in which the network was initially trained on; and (b) test the adaptability of the segmentation network for use in other types of collections. The resilience to data variations from different institutions and the portability of the network across different types of collections are required to confirm its general applicability. The proposed validation method is tested on the Natural History Museum semantic segmentation network, designed to process entomological microscope slides. The proposed semantic segmentation network is evaluated through a series of cross-validation experiments designed to test using data from two types of collections: microscope slides (from three institutions) and herbarium sheets (from seven institutions). The main contribution of this work is the method, software and ground truth sets created for this cross-validation as they can be reused in testing similar segmentation proposals in the context of digitization of natural history collections. The cross-validation of segmentation methods should be a required step in the integration of such methods into image processing workflows for natural history collections.