A method of generating a tomography image includes performing a depth scan on one spot on a surface of a subject using modulated light received from a spatial light modulator, obtaining depth scan data for each of a plurality of patterns of the spatial light modulator by repeating the depth scan on the spot for each of the plurality of patterns, forming a matrix R representing a vector space based on a correlation of signal values of the depth scan data for each of the plurality of patterns, performing a matrix decomposition on the matrix R, dividing the vector space into a noise subspace and a signal subspace based on a matrix obtained by the matrix decomposition, constructing a vector space based on either one or both of components of the signal subspace and components of the noise subspace, and generating a tomography image based on the reconstructed vector space.