Towards a versatile automated cell-detection system for science and diagnostics

Analyzing in-situ tissue structures with complex shapes and textures such as multinuclear cells or cells without nuclei is still a challenge for currently available imageprocessing software. This work aims to provide a versatile system to solve such tasks provided that the structures of interests were detected by immunofluorescence microscopy. Images were automatically acquired using slide-based microscopy. Human domain-experts manually marked up tissue samples to evaluate the performance of the computer generated masks. From precision and recall a balanced F-score was computed to measure the correlation between experts and algorithm output. Exhaustive parameter optimization was conducted to ensure that the optimal input parameters were applied during evaluation of the developed algorithm. This procedure significantly increased the performance compared to manually chosen input parameters. We present an approach that can handle huge tissue areas and does not rely on nuclei detection. Once a markup has been created, the algorithm can be parameter-optimized on ground-truth data for the chosen tissue sample. Thereafter, the resulting settings could be applied automatically to the respective stitched image. Concluding, we provide new insights in physiological and pathopysiological cellular mechanisms by automating the in-situ analysis of proteins in intact tissues.