A 1310 nm spectral/Fourier domain OCT microscope was constructed for in vivo imaging of the rat’s retina9 with 7.5 μm transverse resolution, as shown in Fig. 1. A longer wavelength was used to avoid possible stimulation of the retina by the imaging system.10 The light source consisted of two superluminescent diodes combined, using a fiber coupler to yield a bandwidth of 150 nm. The measured axial (depth) resolution in tissue was 3.8 μm. A spectrometer with a 1024-pixel InGaAs line scan camera (Goodrich Sensors Unlimited, Inc., Princeton NJ) was operated at and controlled by a first computer (PC1). The power of the OCT beam on the sample was 1 mW, and the sensitivity was 96 dB. A square-wave flickering light stimulus was generated for 10 s with a fiber light source (Hg:Xe lamp) and a mechanical shutter controlled by a second computer (PC2). The maximum flicker intensity at the retina was estimated to be , while the minimum intensity between stimuli was . The stimulus spectrum is shown in Fig. 1. Comparable stimulus protocols and experimental designs are frequently used in the literature to study functional hyperemia in the rat retina.4,11,12 Uniform illumination of the retina was confirmed by imaging the retina onto a CCD camera connected to PC2. Repeated OCT volumes for angiography () or Doppler OCT () were acquired during runs of 10 stimuli separated by 25 s. In one run, a stimulus frequency of 12 Hz was used, while in the other run, stimulus frequencies between 6 and 18 Hz were generated in a random order to test for frequency dependence of the response.13 All triggers were collected along with the blood pressure and capnometer readings by a third computer (PC3). Figure 2 shows the asynchronous stimulus and scanning protocol for angiography. Jittered acquisition and stimulation protocols, similar to the ones employed here, are routinely used in fMRI to achieve a higher effective temporal resolution when responses are repeatable14 across trials.