Classical microscopy typically utilizes either a beam and lens or else a scanning probe mechanism to interact with, record , spatially preserve, and amplify the information contained in samples at the microscale. DNA sequencing-based microscopy is a fundamentally different approach to microscopic image formation that utilizes molecular interactions that are recorded in the form of a highly interconnected mesh of unique DNA sequence interactions. The interactions are recorded by means of a DNA polymerization reaction, forming associations between patches of neighboring space, and next gen sequencing is then used to determine the set of neighbor neighbor associations and reconstruct an abstract network containing relative spatial information about the molecules in the sample. We have built a theoretical and computational basis for how this technique achieves image formation, and we describe our current progress in the experimental realization of this technique for protein-targeted 3D reconstruction of biological specimens.