Visualization of cell bodies and neurites in a tB-BABB cleared mouse brain.

Brain sample same as Fig 4; original dataset (LSFM recording, horizontal): same as Fig 4, except for (A). (A) Confocal recording (single plane) from EC layer 3 near the injection site taken after 271 days in clearing solution. Overlay of red channel (rAAV-driven mRFP1 fluorescence, arrows) and green channel (RABVΔG-EGFP fluorescence). Double-infected cells expressing rAAV-driven mRFP1 plus RABVΔG-EGFP fluorescence are indicated by orange to green color (arrowheads). Recording direction: from brain surface (positioned perpendicular to optical axis) to interior. Scale bar, 100 μm. (B) LSFM 50 μm z range maximum projection from a subvolume of the PiC area (RABVΔG-EGFP fluorescence). Arrowheads indicate some Layer 2 neurons, arrows some interneurons. Scale bar, 100 μm. (C) LSFM 50 μm z range maximum z projection from a subvolume of the auditory cortex region (RABVΔG-EGFP fluorescence) showing a cortical layer 5 cell with a big apical dendrite (arrowheads), basal dendrites at the soma, and a basal axon (long arrows). Scale bar, 100 μm. (D) LSFM 90 μm z range maximum projection from a subvolume of the septal area (RABVΔG-EGFP fluorescence) 2.3 mm below brain surface revealing neurite structures (arrowheads). Scale bar, 100 μm. (E) LSFM 20 μm z range maximum projection (RABVΔG-EGFP fluorescence) from a subvolume of the PiC/EC/HC region, showing neurons from cortical EC and the PiC regions and glia from the HC region projecting to the injected EC neurons. Scale bar, 500 μm. (F) Hippocampal DG area enlarged from (E), showing glia cells in the outer granule cell layer (o-gcl) and stratum lacunosum moleculare (LMol), and neurons in the DG hilus region (arrowheads). PiC, Piriform cortex; EC, Entorhinal cortex. Scale bar, 100 μm.