In brief, an unsuppressed rapid water SI (TR = 300 msec) is acquired using the same plane selection, plane thickness, field of view, and spatial resolution as the metabolite SI and a SI is reconstructed for each coil in each subject.
The AGC (automatic gain control) maximum ion time was set to 500 msec (but typically utilized <10 msec) and five " μscans" were acquired for each saved spectrum; thus, the cycle time for each transformed and saved spectrum was about 10 sec.
Spectra were acquired with TR 1,500 msec, TE 144 msec, and a matrix size of 16 × 16 over an FOV of 16 cm, resulting in a scan time of 6.4 min for each region.
High-resolution 3D T1-weighted images were acquired (TR = 1900 msec, TE = 2.15 msec, flip angle = 9°, FOV = 256 mm, 176 slices, 1 mm isotropic voxels).
MEGA-PRESS spectra were acquired using TE = 68 msec (TE1 = 15 msec, TE2 = 53 msec); TR = 1.8 sec; 256 averages; frequency selective editing pulses (14 msec) applied at 1.9 ppm (ON) and 7.46 ppm (OFF).
Serial optical Z-stacks (4 optical planes at 2-µm intervals) of epifluorescent images of RFP-RPGRORF15 and YFP-RPGRIP1α1 were acquired for ∼50 msec and 1×1 binning every 30 minutes for 18.5 hours with a CCD camera (Cascade 512K; Roper Scientific, Trenton, NJ) and Metamorph Software v6.3 (Molecular Devices, Downingtown, PA).
Images were acquired at 500-msec or 1-second intervals; GFP and mRFP were excited sequentially with the 488 and 568-nm lines, respectively.
Spectra were acquired with a 1 msec recycle delay and a time domain of 16 k, with 1000 scans (giving an approximate 1 hour analysis time).
Sagittal whole brain Magnetization Prepared Rapid Acquisition Gradient Echo images were acquired (parameters: TR/TI/TE: 2300/900/2.91 msec; flip angle: 9°; field of view: 256 × 256 mm; slice thickness: 1 mm; resolution: 1 × 1 mm; slices: 176).
Next, the LED was set to illuminate during 0.8 to 0.9 msec of the pulse cycle and two images were acquired in the same manner as before.
