Tissue libraries enable rapid determination of conditions that preserve antibody labeling in cleared mouse and human tissue

Difficulty achieving complete, specific, and homogenous staining is a major bottleneck preventing the widespread use of tissue clearing techniques to image large volumes of human tissue. Borrowing from the success of screening libraries for drug discovery, we created tissue libraries of mouse and human brain sections and a simple image-based quantification routine. We prepared libraries of 500-1000 μm thick tissue sections that are fixed, pre-treated, and cleared via different procedures and then used to optimize staining conditions for a panel of antibodies.

Together, our tissue libraries and image analysis pipeline rapidly determine optimal antibody staining conditions for individual tissues in a cost-effective manner as they use minimal amounts of reagents. Further, these data provide evidence that there is not a universal staining protocol ideal for all antibodies so optimization is necessary to select conditions for multiplexed labelling experiments.

By comparing human and mouse tissue libraries, we found that optimal staining conditions for an individual antibody in mouse tissue correlated well with the optimal conditions for human tissue. This suggests that antibody optimization can be performed in more plentiful mouse tissues to preserve limited human samples for experimental investigation. Finally, we test the optimized conditions on cleared tissue from post-mortem human brain samples with Alzheimer's disease.