First, we define the energy of any voxel outside the valid domain to −1. We define genes as high-quality (in situ data) when they satisfy: average voxel energy > 0.2 and more than 30 voxels higher than 5. This is calculated over the valid domain voxels. The thresholds were based on inspection of the mean versus CV, variance etc. (data not shown). Next, we normalized the voxel energy: for each gene, transform the energy bylog2(voxelenergy(i,in)+1)−ms
