To determine the cell density in the ganglion cell layer (GCL), we counted the somata in 1 to 4 fields (between 74 × 78 and 450 × 474 μm
2) per animal. We selected those frames of the 2P microscopic image stacks with the focal plane in the center of the GCL. Fields with SR101 cell labeling too intense to allow resolution of unlabeled cells were excluded. The GCL cell densities estimated from our counts (
Table 1) matched well the densities previously reported for the mouse retina.
17 For this comparison, we plotted the published GCL cell densities as a function of retinal eccentricity and fitted a Gauss curve,
with density
D (in square millimeters), eccentricity
x (distance from the optic disc in micrometers), and the coefficients
a = 10,017,
b = −4,002.3,
c = 1,916.8, and
w = 713.8. The respective fit parameters for the inner nuclear layer (INL) cell density were
a = 80,568,
b = 30,338,
c = 723.4,
w = 1,005.4. We then compared our ganglion cell layer cell density measured for a certain eccentricity with the density predicted by the Gauss fit (see equation) for the same eccentricity and found no statistically significant difference (Wilcoxon signed test,
n = 17 pairs:
P ≥ 0.32). In the light of this good agreement, we used average densities determined with the equation (for the eccentricity range from 415–1533 μm) to estimate the percentage of damaged cells in GCL and INL (
Table 2). Note that cell density measurements included all somata in the respective layers: ganglion and displaced amacrine cells in the GCL, and amacrine, bipolar, horizontal, and Müller cells in the INL.
To evaluate the anatomic structure and tissue integrity from the 2P image stacks, we determined the density of SR101-filled somata in GCL and INL (
Table 2) as well as the thickness of the different layers (described later;
Table 3). SR-filled cells were counted in at least 8 fields (two eyes; up to 43 fields/nine eyes for the GCL and 35 fields/nine eyes for the INL) per injected drug and time point. For ease of reproducibility and recognition, GCL and inner plexiform layer (IPL) thicknesses were not separately measured but in combination. The INL and outer nuclear layer (ONL) were measured separately, and the vessel plexus was omitted. The number of frames per layer was counted and converted to micrometers corresponding to the layer thickness.