Hydrogels are multi-functional and can be used as scaffolds in bone tissue engineering. The pore architecture of the scaffolds is a significant factor in bone cell function. In this work, oligo (poly (ethylene glycol) fumarate) (OPF) hydrogel is used in the fabrication of porous scaffolds, and the effect of hydrogel porosity on bone formation is evaluated using an in vitro bone marrow stromal cell model. The porous hydrogels consist of copious amounts of water (90% or more by volume), and their structure is very similar to soft tissues. The characterization of porosity and interconnectivity in a typical OPF hydrogel scaffold and the bone formation inside the scaffold are assessed using magnetic resonance microscopy (MRM) techniques and are shown to be very useful in micro structural studies of such water rich materials. A Bruker Avance 7 Tesla (proton 300 MHz) spectrometer equipped with a Micro Imaging 2.5 accessory is used in these studies. By optimizing the acquisition parameters such as relaxation recovery time (TR), echo time (TE), pulse flip angle (TA), and using solvent relaxation-enhancing media, the pores and bone formations are clearly observed at an in-plane resolution of 29 μm/ pixel in various scaffold materials. Analysis of our MRM images shows that the pores are highly interconnected and the porosity computed from the images correlate quite well with the experimental porosity parameters such as porogen size and percentage. In addition, the quantitative alkaline phosphatase activity, alizarin red staining as marker of osteoblastic differentiation, and the mineralization capacity of marrow stromal cells are in good agreement with the bone formation seen in the MRM images.