In high resolution electron microscopy objects are actively altered by the intense electron irradiation that is necessary to reach single atom sensitivity. In these circumstances, a control of beam-sample interactions is no longer a commodity but a necessity. It is of outstanding interest to develop new tools and concepts that strive for a stricter control of the probing electron beam in space and time in order to optimize the detection of every scattering event. This contribution describes research that aims at exploiting the emerging ability to analyze and understand nano-materials with soft and hard matter components by directly determining their atom arrangement in three-dimensions using low-dose rate electron microscopy [1-4]. The approach  mimics best practices in biological research by capturing series of entirely noise dominated images with dose rates that can be smaller than 20 e/Å2s, which are successively reconstructed to obtain in-line holograms with unprecedented contrast and resolution. We observe a variety of previously unknown atom configurations that are otherwise hidden behind a barrier of beam-induced object alterations and capture radiation sensitive structures at atomic resolution that are greatly affected by an exposure of the material to water vapor or other gases in environmental electron microscopy. A further development of time resolved electron microscopy is expected to further accelerate an already rapid progress.