1. A method for generating a multi-dimensional image of a sample, comprising: capturing a first two-dimensional substrate image of a surface region of the sample with a first image capturing modality, wherein locations of at least one material at the surface region are captured; capturing a second two-dimensional substrate image of the surface region with a second image capturing modality which is different from the first image capturing modality, wherein the second image capturing modality provides greater accuracy with respect to locations of at least one material at the surface region than the first image capturing modality; spatially aligning the first two-dimensional substrate image based on the second two-dimensional substrate image; generating a first corrected two-dimensional substrate image based at least in part on the locations of the at least one material in the second two-dimensional substrate image.