Figure 2. DiI–analogues remained in CLARITY–treated nervous tissue and reveal electrode placement.

(a) Multielectrodes painted with either CM-DiI, SP-DiI or FM 1–43FX are inserted from the dorsal side in a sagittal plane into the spinal cord for 10 minutes each. (b) The spine is surgically opened to expose the lumbar spinal cord in the anaesthetized mouse with one electrode array inserted. (c) Illustration of the location of the electrodes tracks covered with different dyes from a sagittal view. (d–e) Widefield images of the hemicords demonstrate that fluorescent DiI–analogues remain in the tissue after CLARITY treatment. FM 1–43FX (right) has the strongest overall fluorescent signal, and CM-DiI (left) has the sharpest traces. (f ) Images of the CLARITY cleared hemisections (broken box) imaged in a drop of 80% glycerol on a glass slide with PFA–fixed spinal cord above for comparison. The hemisections unavoidably curl up into circles. (g) Close up of hemisections imaged with backlighting. The multielectrode had seven shanks, each 50 μm thick and 200 μm apart.