We ultimately seek to understand each interaction at atomic and biological time scales. This goal justifies our pipeline approach, consisting of TR&Ds 1 – 4 (see image and descriptions below) to respectively preserve, read, and interpret macromolecular interactions. One might think of our approach as a “multiscale molecular microscope”. In this analogy, TR&D1 prepares the samples for observation; TR&D2 and TR&D3 enable detailed observation and analysis of the sample; and TR&D4 enables integration of the data into a dynamic and interpretable picture of the sample. Our pipeline produces “classical anatomy at the molecular scale”, isolating and characterizing each component of the machine and ultimately contextualizing it in the specific living environment, so deriving that component’s specific structural functionality. The pipeline builds upon our existing NCDIR work, while incorporating a variety of new methods. It is modular, flexible, and adaptable, so that any investigator can enter and exit at any point, as required by their research priorities; and because of its modularity, researchers will be able to adopt those portions of the pipeline most pressing to their needs and continue to adopt other modules as their research advances.