Aspects of the present application provide methods for analyzing spatially-linked biological samples. The methods may include disposing a spatially-linked biological sample on a surface. The spatially-linked biological sample may be imaged. In certain aspects, nucleic acids from the spatially-linked biological sample may also be analyzed. In some such aspects, the surface can include a plurality of capture sites that contain single-stranded oligonucleotides, and nucleic acids from the spatially-linked biological sample may be captured using at least a subset of the single-stranded oligonucleotides.