A method for determining a set of quantitative three-dimensional surface topography data from images obtained by microscopy, comprising: inputting data representing at least three images obtained by microscopy from a surface of a sample into a data processor, each image having been acquired from the surface with the surface positioned in a different orientation in the microscope relative to an optical axis or a central scanning axis of the microscope; the data processor determining at least a first set of displacements of corresponding points between a first image and a second image and a second set of displacements of corresponding points between the first image and a third image; the data processor fitting directional components in two directions of said first set of displacements to two respective fitting planes, said fitting planes each being defined by parameters of that respective fitting plane, and calculating, from said directional components in each of said two directions, the relative displacements of said corresponding points, said relative displacements each indicating a difference between the displacement of one of said corresponding points and a calculated displacement of a corresponding point on the respective fitting plane; the data processor fitting directional components in two directions of said second set of displacements to two other respective fitting planes, said other fitting planes each being defined by parameters of that respective other fitting plane, and calculating, from said directional components in each of said two directions, the relative displacements of said corresponding points, said relative displacements each indicating a difference between the displacement of one of said corresponding points and a calculated displacement of a corresponding point on the respective other fitting plane; the data processor calculating an orientation of a sample plane for each image and the angle and the axis of rotation of the sample plane with respect to the optical or central scanning axis from the parameters of the fitting planes by requiring that for at least two types of physical parameters, such as orientation of the sample plane in the first image and distances of said corresponding points to the sample plane, the value resulting from said first set of displacements is identical to the value resulting from said second set of displacements; and the data processor calculating at least one set of quantitative three-dimensional surface topography data from the calculated orientation of the sample plane for each image and the angle and axis of rotation of the sample plane and at least said first or second relative displacements. inputting data representing at least three images obtained by microscopy from a surface of a sample into a data processor, each image having been acquired from the surface with the surface positioned in a different orientation in the microscope relative to an optical axis or a central scanning axis of the microscope; the data processor determining at least a first set of displacements of corresponding points between a first image and a second image and a second set of displacements of corresponding points between the first image and a third image; the data processor fitting directional components in two directions of said first set of displacements to two respective fitting planes, said fitting planes each being defined by parameters of that respective fitting plane, and calculating, from said directional components in each of said two directions, the relative displacements of said corresponding points, said relative displacements each indicating a difference between the displacement of one of said corresponding points and a calculated displacement of a corresponding point on the respective fitting plane; the data processor fitting directional components in two directions of said second set of displacements to two other respective fitting planes, said other fitting planes each being defined by parameters of that respective other fitting plane, and calculating, from said directional components in each of said two directions, the relative displacements of said corresponding points, said relative displacements each indicating a difference between the displacement of one of said corresponding points and a calculated displacement of a corresponding point on the respective other fitting plane; the data processor calculating an orientation of a sample plane for each image and the angle and the axis of rotation of the sample plane with respect to the optical or central scanning axis from the parameters of the fitting planes by requiring that for at least two types of physical parameters, such as orientation of the sample plane in the first image and distances of said corresponding points to the sample plane, the value resulting from said first set of displacements is identical to the value resulting from said second set of displacements; and the data processor calculating at least one set of quantitative three-dimensional surface topography data from the calculated orientation of the sample plane for each image and the angle and axis of rotation of the sample plane and at least said first or second relative displacements.