The carboxylate-coated polystyrene latex beads were purchased from ThermoFisher Scientific (Carboxylate-Labeled Microspheres, 0.2 μm, yellow-green fluorescent 505/515, 1% solids). The gel solution was prepared with 12.5 wt% of acrylamide (≥ 99%, Sigma Aldrich, Germany), 0.3 wt% of N,N'-methylenebisacrylamide (≥ 99.5%, Sigma Aldrich, Germany), 0.44 wt% of lithium phenyl-2,4,6-trimethylbenzoylphosphinate photoinitiator (≥ 95%, Sigma Aldrich, Germany), and MQ water. The coverslip was cleaned using UV-ozone treatment for 60 minutes to clean the glass surface. The top coverslip was made hydrophobic using a saline Sigmacote, purchased from Sigma Aldrich, Germany. The gel solution containing nanoparticles was placed within a glass coverslip using imaging spacers. The 0.12 mm thickness with 20 mm well diameter double-sided imaging spacers (Grace Bio-Labs SecureSeal™ imaging spacer) were used for sample preparation. During gelation, a saline Sigmacote-coated coverslip was putted on the top of the sample. After gelation occurred, the top coverslip was carefully removed from the hydrogel due to its hydrophobic properties, and 3D confocal imaging was then acquired as follow. The sample was air-dried for 3 hours and then sputtered with Au/Pd for 60 s (JEOL JFC-1300, Automatic Sputter Coater) prior to the scanning electron microscopy (SEM) imaging. The electron microscopy imaging was performed by using a high-resolution SEM (JSM-7200F field electron SEM).