Here, we provide experimental verification supporting the use of short-section imaging bundles for two-photon microscopy imaging of the mouse brain. The 8 mm long bundle is made of a pair of heavy-metal oxide glasses with a refractive index contrast of 0.38 to ensure a high numerical aperture NA = 1.15. The bundle is composed of 825 multimode cores, ordered in a hexagonal lattice with a pixel size of 14 μm and a total diameter of 914 μm. We demonstrate successful imaging through custom-made bundles with 14 μm resolution. As the input, we used a 910 nm Ti-sapphire laser with 140 fs pulse and a peak power of 9 × 10⁴ W. The excitation beam and fluorescent image were transferred through the fiber imaging bundle. As test samples, we used 1 μm green fluorescent latex beads, ex vivo hippocampal neurons expressing green fluorescent protein and cortical neurons in vivo expressing the fluorescent reporter GCaMP6s or immediate early gene Fos fluorescent reporter. This system can be used for minimal-invasive in vivo imaging of the cerebral cortex, hippocampus, or deep brain areas as a part of a tabletop system or an implantable setup. It is a low-cost solution, easy to integrate and operate for high-throughput experiments.