At day 1 and at week 3 after AION, we performed intracardiac perfusion using 4% paraformaldehyde in phosphate-buffered saline, whole mount retinal dissection, immunohistochemistry, and fluorescence microscopy (Nikon Eclipse TE300 microscope; Nikon Corp., Tokyo, Japan) with ×4, ×10, and ×20 objectives (Nikon Corp.) and commercial software (Metamorph; Molecular Devices, LLC, Sunnyvale, CA, USA). To measure activated microglia at day 1, we performed morphometric analyses of fluorescence signal after immunohistochemistry of whole mount retina using primary rabbit polyclonal anti-Iba1 antibody, which labeled-activated microglia (1:200 dilution; Wako Chemicals, Richmond, VA, USA) and secondary goat anti-rabbit IgG AlexaFluor 568–labeled antibody (1:200 dilution; Life Technologies, Waltham, MA, USA). To count Brn3A
+ RGCs at week 3, we performed whole mount retinal dissection 3 weeks after AION and then stained with primary mouse monoclonal anti-Brn3A antibody (1:200 dilution; Santa Cruz Biotechnology, Dallas, TX, USA) and secondary goat anti-mouse IgG AlexaFluor 568–labeled antibody (1:200 dilution; Life Technologies). All retinal whole mount preparations were mounted with DAPI-containing media (Vectashield; Vector Laboratories, Burlingame, CA, USA). We then used ImageJ (
http://rsbweb.nih.gov/ij/; provided in the public domain by the National Institutes of Health, Bethesda, MD, USA) in a masked setting to quantify Iba1
+ signal in images that were taken using the same parameters under a masked setting. We used a 300-pixel diameter circular region of interest, isolated all particles of interest using the plugin function to analyze particles, and then measured the fluorescence signal for each eye. To quantify Brn3A
+ signal, we took eight images (four quadrants, two images of 0.14 mm
2 each, taken at magnification of ×200) and used a custom-written ImageJ script to quantify and calculate the number of Brn3A
+ cells/mm
2. Only eyes with high-quality imaging at all four quadrants were included in the analysis.