Fluorescent images were collected digitally on a microscope set up for epifluorescence (Microphot FXA; Nikon, Melville, NY). Excitation wavelengths were selected by a computer-controlled filter wheel (Ludl Electronic Products Ltd., Hawthorne, NY). A single-emission filter was used that allows the passage of DAPI (nuclear staining), fluorescent emission wavelengths (TUNEL staining, Alexa 488; Molecular Probes) and (immunocytochemistry, Alexa 594; Molecular Probes), depending on the excitation filter selected, which allowed multiple labels to be captured and the images overlaid without any spatial shifting of the image data. Images were captured with a cooled charge-coupled device (CCD) camera (Photometrics SenSys; Roper Scientific, Tucson, AZ) as 10-bit, 1024 × 1024-pixel, gray-scale images. The camera and microscope automation were computer controlled (IP Laboratory Spectrum; Scanalytics, Fairfax, VA). Images were deconvolved (Microtome plug-in or IP Laboratory Spectrum; Vaytek, Fairfield, IA). Deconvolved images were merged in the computer system to determine relative label distribution, count individual V-1L immunoreactive synapses in defined volumes of retina tissue, and visualize colocalization of labels (TUNEL staining). Images were reconstructed from 12 deconvolved optical sections through a 12-mm-thick vertical cryostat section and were merged in the system software. Tissues from three individual animals for each condition were used in the study, and sections with the same eccentricity (0.5–2 mm lateral to the optic nerve as a reference point) were compared. Orientation of the eye and the retina tissue during processing was maintained by labeling the sclera with a permanent marker and by making asymmetric incision into the retina. Sections from each animal (both the ipsilateral experimental tissue that had been subjected to ischemia and the contralateral control tissue were used from each animal) were analyzed after deconvolution and three-dimensional reconstruction (as just described); six Z-stacked images for each condition were quantified. Immunoreactive profiles were counted by using automated image acquisition and intensity analysis software (SimplePCI; Compix Inc., Cranberry Township, PA). Software parameters that were used to identify immunoreactive profiles (fluorescence intensity, area, volume) were kept constant for all analyses of different experimental conditions. Results are expressed in number of immunoreactive profiles per unit volume. Statistical analysis of immunoreactive labels and of the TUNEL assays was performed on computer by paired t-test (SPSS; SPSS Science Inc., Chicago, IL).