BrainFilm, a novel technique for physical compression of 3D brain slices for efficient image acquisition and post-processing

Tissue clearing enables us to observe thick tissue at a single cell resolution by reducing light scattering and refractive index matching. However, imaging of a large volume of tissue for 3D reconstruction requires a great deal of time, cost, and efforts. Few methods have been developed to transcend these limitations by mechanical compression or isotropic tissue shrinkage. Tissue shrinkage significantly lessens the imaging burden; however, there is an inevitable trade-off with image resolution. Here, we have developed the “BrainFilm” technique to compress cleared tissue at Z-axis by dehydration, without alteration of the XY-axis. The Z-axis compression was approximately 90%, and resulted in substantial reduction in image acquisition time and data size. The BrainFilm technique was successfully used to trace and characterize the morphology of thick biocytin-labelled neurons following electrophysiological recording and trace the GFP-labelled long nerve projections in irregular tissues such as the limb of mouse embryo. Thus, BrainFilm is a versatile tool that can be applied in diverse studies of 3D tissues in which spatial information of the Z-axis is dispensable.