Table 3. Measurements of rod outer segments in P30 mice with increasing rhodopsin expression.

Copy Number	Genotype	Widtha(µm)	Lengtha(µm)	Disks/µma	Incisuresa(µm)
1	mRho+/−	1.1±0.2	27.1±4.1	26.4±0.9	0.8±0.4
2	mRho+/+	1.5±0.2	32.1±4.6	25.2±1.2	0.7±0.2
3	mRho+/+NHRE+/0	1.8±0.2	40.1±4.2	24.3±0.9	0.6±0.2
4	mRho+/+NHRE+/+	2.2±0.4	35.8±3.9	25.3±0.9	0.5±0.3
1+P23H	mRho+/−P23H+/0	1.4±0.3	7.3±2.4
2+P23H	mRho+/+P23H+/0	1.8±0.4	13.1±2.9
3+P23H	mRho+/+NHRE+/0P23H	2.1±0.4	15.0±4.0

^aBoxer from EMAN [49] was used to measure the rod outer segment length, width, and incisure length. For width, we used longitudinal sections through the outer segments (see middle panels in Figures 4 and 7) and measured the widest section of the outer segment. Since most rods are cut at some angle relative to their long axis, this method helps to ensure an accurate measure of width. For each genotype, we made 20 measurements from multiple sections for each mouse and averaged the measures from 3 different mice. For length, we used low magnification images of longitudinal sections such as those shown in the top panels in Figures 4 and 7. We used the thickness of the rod outer segment layer, as measured along a line parallel to the primary orientation of the rod outer segments, as an indicator of the average length of rod outer segments. For each genotype, we made 20 measurements from multiple sections for each mouse and averaged the measures from 3 different mice. The linear density of disks along the length of the rod outer segment was measured by counting the number of disks per micron in images like those in the middle panels of Figure 4. For incisure lengths, we chose sections such as those in the bottom panels in Figure 4, and measured lengths in those sections where an incisure was readily visible. For 2 Rho and 3 Rho mice, we also looked for sections where the striations from mis-oriented disks were minimal; this was not possible for 1 Rho and 4 Rho mice, which displayed a more striated appearance than 2 Rho or 3 Rho mice. For each genotype, we made 10 measurements of incisure length for each mouse and averaged the measurements from 3 different mice. In all cases, the measurements were averaged and the standard deviation was determined.