Modern next-generation high-performance materials designed with complex 3D heterogeneous architectures and chemistry can be grown with controllable precision down to nanometer or atomic length scales (e.g. surfaces, interfaces or defects). Unfortunately, visible light and X-ray sources lack the capability to resolve features below nano-meter length scales due to fundamental limitations in wavelengths. Through the development of aberration correctors in scanning transmission electron microscopes (S/TEM), material structure can be routinely imaged at sub-nanomaterial resolutions. However, the necessary high electron doses and low signal to noise ratios prevents the general characterization spectroscopy of materials. Thus, advanced spectroscopy and especially 3D chemical tomography is only performed on specimens that can withstand the beam irradiation. In this talk, I will demonstrate how we can link modern optimization frameworks with S/TEM imaging to investigate 3D material structure and chemistry at novel resolutions and time scales than previously possible. Specifically, I will show that through the concept of data fusion and linking of modalities that are simultaneously acquired collected inside the electron microscope enables low-dose spectroscopy at radiation levels orders of magnitude lower than conventionally possible. Conjoined with contributions in a popular open source volumetric rendering software (tomviz.org) - electron tomography can now occur simultaneously with data collection allowing researchers to diagnose 3D structure in real time while operating the microscope.