A method of preparing a crystalline contrast agent for magnetic resonance imaging from a zwitterionic carboxylic pyridyl ligand includes mixing metal ion and the pyridyl ligand and obtaining crystals therefrom. The crystalline contrast agent includes a manganese-organic or gadolinium-organic 3D framework. The crystalline contrast agent is employed in a kit and a pharmaceutically acceptable composition. The method allows for preparing crystalline contrast agents with superior properties with easily available starting materials and with an economic and efficient process. The method allows for preparing crystalline contrast agents with exceptional water-stability and water-solubility, which exhibit high longitudinal relaxivities and with excellent stabilities under physiological conditions and low cytotoxicity. Further provided is a method for in vivo imaging of a subject, in particular a human, comprising administering the crystalline contrast agent to the subject.