A multiple depth optical coherence tomography system for imaging positions at multiple depth positions in a sample, the OCT system comprising: a light source (2, 3, 302) for providing a beam of light; an optical path comprising: a) a sample arm (5, 8, 310) configured to propagate the beam of light from a beam splitter (6, 13, 52, 304, 330) to the sample and to direct a sample return light comprising a first return light beam reflected from a first position in the sample and a second return light beam reflected from a second position in the sample, the second return light having a second dispersion level that is larger than a first dispersion level of the first return light beam by a dispersion difference amount; b) a first reference arm (7, 14, 334) configured to produce a first reference light beam at the first dispersion level and a second reference arm (9, 16, 336) configured to produce a second reference light beam at the second dispersion level; and c) one or more optical elements (13, 25, 22, 32, 34, 52, 310, 312, 330) configured to combine all of the sample return light, the first reference light beam and the second reference light beam and to direct the combined beams; and an OCT detector (11, 36, 328) configured to measure an interferogram based on the combined beams, whereby the measured interferogram encodes a component corresponding to the first position and a component corresponding to the second position, characterised in that the OCT system is further configured to estimate the dispersion difference amount and to decode the imaging information for both the first position and the second position based on the estimated dispersion difference amount. a light source (2, 3, 302) for providing a beam of light; an optical path comprising: a) a sample arm (5, 8, 310) configured to propagate the beam of light from a beam splitter (6, 13, 52, 304, 330) to the sample and to direct a sample return light comprising a first return light beam reflected from a first position in the sample and a second return light beam reflected from a second position in the sample, the second return light having a second dispersion level that is larger than a first dispersion level of the first return light beam by a dispersion difference amount; b) a first reference arm (7, 14, 334) configured to produce a first reference light beam at the first dispersion level and a second reference arm (9, 16, 336) configured to produce a second reference light beam at the second dispersion level; and c) one or more optical elements (13, 25, 22, 32, 34, 52, 310, 312, 330) configured to combine all of the sample return light, the first reference light beam and the second reference light beam and to direct the combined beams; and a) a sample arm (5, 8, 310) configured to propagate the beam of light from a beam splitter (6, 13, 52, 304, 330) to the sample and to direct a sample return light comprising a first return light beam reflected from a first position in the sample and a second return light beam reflected from a second position in the sample, the second return light having a second dispersion level that is larger than a first dispersion level of the first return light beam by a dispersion difference amount; b) a first reference arm (7, 14, 334) configured to produce a first reference light beam at the first dispersion level and a second reference arm (9, 16, 336) configured to produce a second reference light beam at the second dispersion level; and c) one or more optical elements (13, 25, 22, 32, 34, 52, 310, 312, 330) configured to combine all of the sample return light, the first reference light beam and the second reference light beam and to direct the combined beams; and an OCT detector (11, 36, 328) configured to measure an interferogram based on the combined beams, whereby the measured interferogram encodes a component corresponding to the first position and a component corresponding to the second position, characterised in that the OCT system is further configured to estimate the dispersion difference amount and to decode the imaging information for both the first position and the second position based on the estimated dispersion difference amount.