Fig. 1. Schematic representation of ClearAIM: (a) optical setup; (a*) enlarged sample; (b) sample preparation scheme.

Fig. 2. ClearAIM data processing algorithm: (a) object mask generation; (b) metrics calculation.

Fig. 3. Results of the ClearAIM method for experimentally monitoring the optical clearing process (CUBIC-R1 solution) on exemplifying mouse brain tissue slices of (a1), (a2) 500 µm and (b1), (b2) 1 mm. Visualization 1 and Visualization 2 provide time-lapse clearing process examination for the 500-μm- and 1-mm-thick slices, respectively. Plots show the (c) transparency, (d) relative area, and (e) overlapped normalized area and normalized transparency for both slices over the course of 71 h.

Fig. 4. Results of quantitative monitoring of the additional four slices: two 500 µm thick slices and two 1 mm thick slices (Visualization 3, Visualization 4, Visualization 5, and Visualization 6).

Fig. 5. Representative images of 500-μm-thick brain slices after (a) 1-day and (b) 3-day CUBIC-R1 incubation at equivalent imaging depths under identical acquisition conditions. The scale bar is 100 µm, and the green boxes on the right represent zoomed areas. (c) The plot shows the mean (averaged) background intensity across a 400 µm imaging range (total n=6 samples).