Due to a high heterogeneity in pose and size and to a limited number of available data, segmentation of pediatric images is challenging for deep learning methods. In this work, we propose a new CNN architecture that is pose and scale invariant thanks to the use of Spatial Transformer Network (STN). Our architecture is composed of three sequential modules that are estimated together during training: (i) a regression module to estimate a similarity matrix to normalize the input image to a reference one; (ii) a differentiable module to find the region of interest to segment; (iii) a segmentation module, based on the popular UNet architecture, to delineate the object. Unlike the original UNet, which strives to learn a complex mapping, including pose and scale variations, from a finite training dataset, our segmentation module learns a simpler mapping focusing on images with normalized pose and size. Furthermore, the use of an automatic bounding box detection through STN allows saving time and especially memory, while keeping similar performance. We test the proposed method in kidney and renal tumor segmentation on abdominal pediatric CT scanners. Results indicate that the estimated STN homogenization of size and pose accelerates the segmentation (25h), compared to standard data-augmentation (33h), while obtaining a similar quality for the kidney (88.01% of Dice score) and improving the renal tumor delineation (from 85.52% to 87.12%).