Improving Unsupervised Stain-To-Stain Translation using Self-Supervision and Meta-Learning

In digital pathology, many image analysis tasks are challenged by the need for large and time-consuming manual data annotations to cope with various sources of variability in the image domain. Unsupervised domain adaptation based on image-to-image translation is gaining importance in this field by addressing variabilities without the manual overhead. Here, we tackle the variation of different histological stains by unsupervised stain-to-stain translation to enable a stain-independent applicability of a deep learning segmentation model. We use CycleGANs for stain-to-stain translation in kidney histopathology, and propose two novel approaches to improve translational effectivity. First, we integrate a prior segmentation network into the CycleGAN for a self-supervised, application-oriented optimization of translation through semantic guidance, and second, we incorporate extra channels to the translation output to implicitly separate artificial meta-information otherwise encoded for tackling underdetermined reconstructions. The latter showed partially superior performances to the unmodified CycleGAN, but the former performed best in all stains providing instance-level Dice scores ranging between 78% and 92% for most kidney structures, such as glomeruli, tubules, and veins. However, CycleGANs showed only limited performance in the translation of other structures, e.g. arteries. Our study also found somewhat lower performance for all structures in all stains when compared to segmentation in the original stain. Our study suggests that with current unsupervised technologies, it seems unlikely to produce generally applicable fake stains.

CNN Cascades for Segmenting Whole Slide Images of the Kidney

Due to the increasing availability of whole slide scanners facilitating digitization of histopathological tissue, there is a strong demand for the development of computer based image analysis systems. In this work, the focus is on the segmentation of the glomeruli constituting a highly relevant structure in renal histopathology, which has not been investigated before in combination with CNNs. We propose two different CNN cascades for segmentation applications with sparse objects. These approaches are applied to the problem of glomerulus segmentation and compared with conventional fully-convolutional networks. Overall, with the best performing cascade approach, single CNNs are outperformed and a pixel-level Dice similarity coefficient of 0.90 is obtained. Combined with qualitative and further object-level analyses the obtained results are assessed as excellent also compared to recent approaches. In conclusion, we can state that especially one of the proposed cascade networks proved to be a highly powerful tool for segmenting the renal glomeruli providing best segmentation accuracies and also keeping the computing time at a low level.