Optical coherence tomography (OCT) images the back of the eye in cross-section using light, a little like ultrasound but with light waves instead of sound. It is one of the most-used tools in modern ophthalmology. Drag the slider below to scan across the macula and watch the foveal pit form.
OCT uses low-coherence interferometry to resolve the neurosensory retina at roughly 5 micron axial resolution. Each A-scan measures the echo time-delay of reflected light; a B-scan is a lateral series of A-scans, and a macular cube stacks B-scans for thickness mapping. Drag the slider to move the B-scan across the cube and watch the foveal contour deepen toward the umbo.
The macula is the small central patch of retina responsible for your sharp, detailed, central vision, the vision you use to read this sentence. At its very center sits the fovea, where cone photoreceptors are packed most densely. To give light a clear path to those cones, the inner retinal layers are swept aside, leaving a shallow depression. That depression is the foveal pit, and it is the landmark you watched form in the scan above.
An OCT cross-section, called a B-scan, shows the retina as a stack of bands. Near the top is the inner retina (the nerve fiber and ganglion cell layers that carry signals toward the brain). Below it lie the photoreceptors, the rods and cones that capture light. At the base is the retinal pigment epithelium (RPE), a supportive layer that appears as a bright line. The thickness and integrity of each band is what a clinician reads.
A healthy fovea has a clean, well-formed pit. When fluid collects in the macula, the pit fills in and the layers swell; when photoreceptors are lost, the bands thin or break up. Because OCT captures all of this in seconds and without touching the eye, scrolling through these cross-sections has become a daily skill in the clinic, and a place where careful, quantitative reading, the same habit I bring to genomic data, makes a real difference.
OCT relies on low-coherence interferometry: light is split between a reference arm and the eye, and the interference of returning light encodes depth. Spectral-domain (SD-OCT) captures a full depth profile at once at roughly 5 micron axial resolution; swept-source (SS-OCT) uses a tunable laser for deeper, faster imaging. A B-scan is a lateral series of A-scans; a macular cube stacks B-scans, which segmentation software turns into the ETDRS thickness map and the central subfield thickness.
From inner to outer: internal limiting membrane (ILM), retinal nerve fiber layer (RNFL), ganglion cell layer (GCL), inner plexiform layer (IPL), inner nuclear layer (INL), outer plexiform layer (OPL), outer nuclear layer (ONL), external limiting membrane (ELM), ellipsoid zone (EZ), interdigitation zone, and retinal pigment epithelium (RPE) over Bruch's membrane. At the foveola the inner layers (RNFL through INL) are displaced centrifugally, leaving a cone-rich photoreceptor layer and Muller cells. This is the anatomic basis of the foveal pit and of peak visual acuity.
The cross-section makes disease legible: intraretinal cysts and increased central subfield thickness in diabetic macular edema; a full-thickness defect with loss of the foveal contour in a macular hole; a hyperreflective, wrinkled inner surface in epiretinal membrane; drusen as RPE undulations, geographic atrophy as RPE and EZ loss, and sub- or intraretinal fluid in exudative AMD. Ellipsoid-zone integrity is a useful structural correlate of visual potential.
Normative color maps invite "red disease" and "green disease": over-reading a red flag in a healthy eye, or being falsely reassured by green, especially in high myopia, tilted discs, or with segmentation error. I wrote about exactly this failure mode for color-coded RNFL analysis in Eye (2026). Always read the underlying B-scan, not just the map, and check signal strength and segmentation before trusting a number.
I work where RNA bioinformatics meets the eye clinic.