For immunofluorescence analysis, cryostat sections were incubated in HistoVT One (1:10 dilution, 30 minutes at 70°C; Nacalai, Inc., San Diego, CA, USA) for antigen retrieval, washed with PBS (phosphate-buffered saline: 0.1 M NaCl, 0.05 M Na-phosphate buffer, pH 7.2), and blocked for at least 30 minutes in 10% donkey serum. Primary antibodies were rabbit anti-hPAP (SP15, 1:50; Epitomics, Burlingame, CA, USA); mouse anti-PKCα (protein kinase C α) (1:100; Stressgen [now Enzo Life Sciences, Plymouth Meeting, PA, USA]); mouse anti-rhodopsin
48 (rho1D4, 1:100; gift of Robert S. Molday, University of British Columbia); mouse anti-recoverin
49 (1:500; gift of James F. McGinnis, University of Oklahoma); mouse anti-Bassoon (1:600; Stressgen); mouse anti-calbindin (1:500; Sigma-Aldrich Corp.); mouse anti-PSD95 (1:500; Stressgen); mouse anti-HPC1
50 (1:500; gift of Colin J. Barnstable, now Penn State College of Medicine); mouse anti-calcium-calmodulin kinase II (CamKII, 1:100; Chemicon, Temecula, CA, USA [now EMD Millipore]); rabbit anti-Iba1 (1:100; Biocare Medical, Concord, CA, USA); rabbit anti-CRALBP (cellular retinaldehyde binding protein)
51 (1:1000; gift of John C. Saari, University of Washington); and rabbit anti-GFAP (glial fibrillary acidic protein) (1:50; Chemicon). Primaries were left on sections overnight at 4°C. After several PBS washes, slides were incubated for at least 30 minutes at room temperature in fluorescent secondary antibodies (dilution of 1:200–1:400), Alexa Fluor 488 donkey anti-rabbit IgG (H+L) and rhodamine X donkey anti-mouse IgG (H+L) (Jackson Immuno Research, Westgrove, PA, USA). Sections were then washed with PBS, coverslipped using Vectashield mounting media (Vector Labs, Burlingame, CA, USA) with 5 μg/mL 4′,6-diamidino-2-phenylindole (DAPI), and imaged using an Olympus BXH10 (Cypress, CA, USA), Nikon FXA microscope (Nikon Instruments, Melville, NY, USA), or a Zeiss LSM700 confocal microscope (Carl Zeiss Microscopy GmbH, Oberkochen, Germany), taking stacks of 5- to 8-μm thickness at ×20, ×40, and ×63 (selected images). Zen 2012 software (
https://www.zeiss.com/microscopy/us/downloads/zen.html; in the public domain) was used to extract confocal images. Three-dimensional (3D) images were extracted separately for each channel and combined in Adobe Photoshop CS6 software (San Jose, CA, USA). In addition, Volocity (x64) software (Perkin-Elmer,
www.cellularimaging.com; in the public domain) was used to obtain higher-magnification 3D opacity-rendered images that could be rotated for better viewing of 3D structures such as cell bodies and cellular processes. These images were also used to determine if labels were colocalized in certain locations.