Objective: Image reconstruction in high resolution PET scanners with depth of interaction (DOI) capability is computationally challenging due to the high sampling in detector and image space. This study evaluates the use of a virtual cylinder to reduce the number of lines of response (LOR) for DOI-based reconstruction while maintaining uniform sub-millimetre spatial resolution. Approach: Virtual geometry was investigated using the awake animal mousePET as a test case. Using GATE, we simulated the physical scanner and three virtual cylinder implementations with detector size 0.7405 mm, 0.4712 mm and 0.3575 mm. The virtual cylinder condenses physical LORs stemming from various crystal pairs and DOI combinations, and which intersect a single virtual detector pair, into a single virtual LOR. Quantitative comparisons of the point spread function (PSF) at various positions within the field of view (FOV) were compared for reconstructions based on the vPET implementations and the physical scanner. We also assessed the impact of the anisotropic PSFs by reconstructing images of a micro Derenzo phantom. Main results: All virtual cylinder implementations achieved LOR data compression >50%. PSF anisotropy in radial/tangential profiles was chiefly influenced by DOI resolution. Spatial degradation introduced by virtual cylinders was most prominent axially. All virtual cylinders achieved sub-millimetre volumetric resolution across the FOV using 6-bin DOI reconstructions (3.3 mm DOI resolution). Using 0.4712 mm detectors with 6 DOI bins (LOR compression 86%) yielded nearly identical reconstructions to the non-virtual case. Significance: Our results show that DOI PET reconstruction with 50-86% LOR compression and sub-millimetre spatial resolution is possible using virtual cylinders. The methodology and analysis can be extended to high resolution scanners with DOI capability.