Multispectral autofluorescent and immunofluorescent datasets were collected from whole-mount eyecups, retinal cryosections, and enriched melanosome fractions by using the 63× oil, plan apochromat, 1.4-NA objective on a spectral deconvolution scanning laser confocal microscope (model FV1000; Olympus, Lake Success, NY), equipped with violet diode (405 nm), argon-ion (457/488/514 nm), krypton-ion (563 nm), and helium-neon ion (633 nm) lasers. Four independent photomultipliers (PMTs) were used for detection of emission spectra. Laser intensity, pinhole diameter, PMT gain, PMT black level, scan speed, and image size were constant for each excitation wavelength between experiments. Laser irradiance levels at the plane of the sample were: 2.5 (405 nm), 1.4 (488 nm), 6 (633 nm), and 1.5 (563 nm) mW. Acquisition was controlled via the integrated software (FluoView; Olympus) software.
AF datasets were acquired at 633-nm excitation, and emission spectra were collected at 10-nm intervals between 700 and 800 nm, using the λ scan function in blind mode. This spectral deconvolution function utilizes calibrated diffraction gratings to provide a variable band-pass emission filter with 2-nm spectral resolution. AF datasets were acquired at 488-nm excitation and emission spectra collected between 500 and 600 nm, 600 and 700 nm, 700 and 800 nm, or 730 and 760 nm. In both cases, emission spectra were collected at wavelengths sufficiently distant from the excitation light to prevent contamination of the emission signals by reflected excitation light. Emission spectra from fluorescent probes were acquired sequentially using the 405/488/563-nm laser lines with the following emission band-pass filters: DAPI (peak 447/BP 60), FITC-phalloidin (536/40), and Alexa Fluor 594 (624/40). Image datasets with associated metadata were exported as 12-bit.oib files. Image analysis, 3-D reconstruction, and montaging were performed with two image-analysis programs (ImageJ; developed by Wayne Rasband, National Institutes of Health, Bethesda, MD; available at http://rsb.info.nih.gov/ij/index.html, and Photoshop CS3; Adobe Systems, Inc., San Jose, CA).