Extended Data Fig. 2: Characterization of spinal cord-projecting neurons across the whole brain during recovery from SCI.

a, Uninjured mice, and mice 1 (acute) and 8 weeks (chronic) (n = 3 mice per group) after left lateral hemisection at T10 were examined. G-deleted rabies was injected into the left (ipsilesional) lumbar spinal cord. Representative injection site of the left lumbar spinal cord demonstrating laterality of the injection. Demonstration of the whole brain clearing and imaging pipeline for mice injected with rabies. CLARITY was utilized due to its ability to preserve endogenous fluorescence, followed by imaging with a custom-built mesoSPIM lightsheet microscope²². Whole mouse brain registration was performed using MIRACL^19,20. Optical sections demonstrating registration of the mouse Allen Brain Atlas on raw CLARITY data of a mouse brain. Representative visualization of labeled neurons with subsequent semi-automated segmentation of neurons using the Arivis Vision 4D three-dimensional analysis software. b, 3D visualization of whole brain labeling of all neurons with direct connections to the lumbar spinal cord. Representative whole brain of uninjured animal with optical sections highlighting labeling in key regions of the brain. c, 3D representations of all brains used in the analysis of whole brain connectivity with time after SCI including uninjured mice and mice 1 week and 8 weeks after injury. The lateral hypothalamus is highlighted with optical sections.