Imaging:

Magnetic resonance imaging was performed at 4ºC using an 11.7 Tesla, vertical bore (89 mm) Bruker Avance microimaging system (Bruker Instruments, Billerica, MA). We used a shielded gradient set (max 100 gauss/cm gradient strength) with home-built RF probes of various sizes (3-20 mm) and configurations (solenoid and birdcage). Images used to create the atlas were recorded using 3D multispin echo protocols (one to eight echoes). Typical spatial resolution was 20 to 80 microns per voxel, depending on the size of the embryo. We typically collected a number of different types of images for each sample - both T2 and T1 weighted. T2-weighted images were recorded using 3D multispin echo protocols [TR = 2 sec, TE = 25 to 200 ms]. T1 weighted images [TR = 200-400 ms and TE= 6 ms] had significantly less contrast than T2 weighted images.