Electron Microscopy Data Bank (EMDB) provides biological researchers with a platform for uploading and downloading data obtained mainly by electron microscopy. With the continuous expansion of the total amount of data stored in EMDB in recent years, its influence has also been continuously improved. In order to make it easier for domain scientists to make better use of these data, we analyzed the EMDB meta-information structure and developed a visual analytics system, called VASEM, to provide convenient data exploration, searching, and analysis tools. Domain scientists can use our system to interactively filter massive EMDB data into relatively small subset for analysis and obtain subset depiction from visualization results. A modified parallel coordinates plot suitable for large-scale multi-dimensional ranking data visualization is also proposed for EM data subset depiction tasks. We present two usage scenarios to describe how the proposed system achieves the design goals.