Four to five millimeter thick hippocampal and amygdaloid slices were cleared based on the protocol described by Ye et al. (2016) (link)). Briefly, >10 weeks old mice were transcardially perfused with ice cold phosphate-buffered saline (PBS) followed by 4% paraformaldehyde (PFA), brains were removed and kept in 4% PFA overnight at 4°C. Brains were then transferred to a hydrogel solution (PBS with: 2% acrylamide, bio-rad #161-0140; 0.1% Bisacrylamide, bio-rad #161-0142; 0.25% VA-044 initiator, Wako, 011-19365; 4% PFA) for 2 days. The samples were then degassed with N2 for 45 min and polymerized in 37°C for 3.5 hr. The samples were then washed overnight in 200 mM NaOH-Boric buffer (sigma, #B7901) containing 8% sodium dodecyl sulfate (SDS) (sigma, #L3771), to remove PFA residuals. Samples were then stirred in a clearing solution (100 mM Tris-Boric buffer, bio-lab, #002009239100 with 8% SDS) at 37°C for 3–4 weeks. After the samples became transparent, they were washed with PBST (PBS with 0.2% tritonX100; ChemCruz, #sc-29112A) for 24 hr at 37°C with mild shaking and for another 24 hr with fresh PBST 0.2% at RT. Finally, the samples were incubated in the refractive index matched solution Rapiclear (RI = 1.47; SunJin lab, #RC147002) for 10 hr at 37°C and 2 days at room temperature before imaging.