Automated image analysis in large-scale cellular electron microscopy: A literature survey

Large-scale electron microscopy (EM) datasets generated using (semi-) automated microscopes are becoming the standard in EM. Given the vast amounts of data, manual analysis of all data is not feasible, thus automated analysis is crucial. The main challenges in automated analysis include the annotation that is needed to analyse and interpret biomedical images, coupled with achieving high-throughput. Here, we review the current state-of-the-art of automated computer techniques and major challenges for the analysis of structures in cellular EM. The advanced computer vision, deep learning and software tools that have been developed in the last five years for automatic biomedical image analysis are discussed with respect to annotation, segmentation and scalability for EM data. Integration of automatic image acquisition and analysis will allow for high-throughput analysis of millimeter-range datasets with nanometer resolution.