Confocal microscopy has been a standard tool to acquire 3D fluorescence biological images at sub-micron resolution. The scattering effects in turbid tissue and the specifications of high N.A. objective lens limit the image dimensions, so the confocal microscopy frequently provides images for micro-anatomy. However, the high quality large volume tomography is still desired to provide correlative images between micro- and macro-anatomy. In this presentation, we extend the dimensions of micro-image at single-cell resolution from tens micrometer levels to multi-millimeter levels by integrating steps of tissue clearing, vibratome sample sectioning, stepper image stitching, and confocal imaging techniques, and we named this system as Serial Tiled-Z axial (STZ) tomography. Mapping the whole-body connectome, a wiring diagram of the entire nervous system is the first application of STZ tomography and provides the whole body neural circuits for governing internal body functions and external behaviors. STZ tomography generates high-resolution in situ datasets for accurate registration of structural and functional data collected from different individuals into a common three-dimensional space for big data storage, search, sharing, analysis, and visualization. Inserting a super resolution module, STZ tomography opens the door to super resolution imaging of routine systematic neuroanatomy of large tissues, such as the whole mouse and human brain. The second application is to map tumor tissue samples which are free from distortion problem from dehydration in the H&E protocol.