Highly focused Micro-SPECT scanners enable the acquisition of functional small animal data with very high-resolution. To acquire a maximum of emitted photons from a specific structure of interest and at the same time minimize the required acquisition time, typically only a small subvolume of the animal is scanned that contains the organs of interest. This Volume of Interest (VOI) can be defined manually based on photographs of the animal taken prior to SPECT scanning, for example two lateral views and a top view. In these photographs however, only the surface of the animal is visible and therefore visual estimation of the location of these organs may be difficult. In this paper, we propose a novel atlas-based technique for estimating the organ VOI for the major organs by mapping a small animal atlas to optical scout images. The user is required to outline the animal contour in one lateral view, and to mark two lateral landmarks in the top view photograph. These landmarks subsequently serve as fiducial landmarks to define a 3D Thin-Plate-Spline mapping of an anatomical mouse atlas to the photographic coordinate space. Planar projections of the mapped atlas organs on the photographs greatly facilitate the estimation of the size and position of the target organ. To validate the proposed approach, the estimated organ VOIs were compared to manually drawn organ outlines in a Micro-CT scan, which was co-registered to the scout photographs using physical landmarks. The results demonstrate a highly promising volume correspondence between the real and the estimated organ VOIs.