MicroSPECT systems providing high resolution and high sensitivity are often based on imaging a mouse inside a tube with many pinholes. Projection images from a small target region, e.g., heart or brain, can be recorded simultaneously on multiple detectors with little multiplexing since each pinhole aperture can be restricted to view just the target region; however, this often requires that much of the mouse body be scanned through the target region of the collimating tube to obtain complete data for reconstruction. We describe another approach for joint reconstruction of both low- and high-resolution projection data acquired sequentially through many rectangular pinholes embedded in two tungsten tube sections of different diameter, placed end-to-end along the axis of a 3-head clinical SPECT scanner. One section provides a whole-body scout image of good sensitivity, but limited resolution, for locating the primary organ of interest and acquiring complete data for reconstruction. A second, 'hi-res' section, which contains many smaller pinholes, is then moved into place axially over the mouse, which is also moved to position its target organ in the center of the gantry. We optimized a scout section for a Trionix triple-head SPECT system to provide minimum mean-squared error of reconstructed voxel counts throughout a ∼6-cm axial range, with the constraints of fixed 2.4-mm scout system resolution, limited multiplexing, and no detector motion. The optimal radial distance to the closest scout pinhole and optimal number of MLEM iterations were 4.4 cm and 60 iterations, respectively; radial distances of the 30 pinholes ranged from 4.4 to 4.8 cm. After including whole-body mouse reconstructions of simulated 30-pinhole scout data into reconstructions of data from 93, 0.33-mm pinholes in a hi-res section viewing the heart region, we obtained high-resolution images of the heart, embedded in lower resolution images of the body, with minimal artifacts.