A method for providing a composite image of a single biological sample, comprising the steps of: generating a first image of the biological sample, comprising the steps of: a. contacting the sample on a solid support with a first binder for a target protein; b. staining the sample with a fluorescent marker that provides morphological information; c. detecting, by fluorescence, signals from the first binder and the fluorescent marker; d. generating the first image of at least part of the sample from the detected fluorescent signals; and then generating a second image of the biological sample, comprising the steps of: a. contacting the same sample from step with a probe for each of at least one target nucleic acid sequence thus hybridizing the probes with the target nucleic acid sequence; b. optionally, staining the sample with the fluorescent marker; c. detecting, by fluorescence, signals from the probes for each of the target nucleic acid sequences and the fluorescent marker; and d. generating the second image of at least part of the sample from the detected fluorescent signal; and generating a composite image that provides the relative location of both the target protein and the target nucleic acid; wherein said composite image allows direct comparison of results obtained from the first image with that from the second image on a cell by cell basis, wherein generation of the composite image comprises: a) using signal information acquired in the generation of the first image and the generation of the second image to generate the composite image; or b) registering the location of signals from the fluorescent marker acquired in step 1 with the location of signals from the fluorescent marker acquired in step 2, and wherein step (d) comprises, (i) generating an initial image of at least part of the sample from the detected fluorescent signals; and (ii) selecting a region of interest from the initial image, and detecting by fluorescence, signals from at least the first binder and the fluorescent marker to generate the first image at a higher resolution than the initial image. generating a first image of the biological sample, comprising the steps of: a. contacting the sample on a solid support with a first binder for a target protein; b. staining the sample with a fluorescent marker that provides morphological information; c. detecting, by fluorescence, signals from the first binder and the fluorescent marker; d. generating the first image of at least part of the sample from the detected fluorescent signals; and then a. contacting the sample on a solid support with a first binder for a target protein; b. staining the sample with a fluorescent marker that provides morphological information; c. detecting, by fluorescence, signals from the first binder and the fluorescent marker; d. generating the first image of at least part of the sample from the detected fluorescent signals; and then generating a second image of the biological sample, comprising the steps of: a. contacting the same sample from step with a probe for each of at least one target nucleic acid sequence thus hybridizing the probes with the target nucleic acid sequence; b. optionally, staining the sample with the fluorescent marker; c. detecting, by fluorescence, signals from the probes for each of the target nucleic acid sequences and the fluorescent marker; and d. generating the second image of at least part of the sample from the detected fluorescent signal; and a. contacting the same sample from step with a probe for each of at least one target nucleic acid sequence thus hybridizing the probes with the target nucleic acid sequence; b. optionally, staining the sample with the fluorescent marker; c. detecting, by fluorescence, signals from the probes for each of the target nucleic acid sequences and the fluorescent marker; and d. generating the second image of at least part of the sample from the detected fluorescent signal; and generating a composite image that provides the relative location of both the target protein and the target nucleic acid; a) using signal information acquired in the generation of the first image and the generation of the second image to generate the composite image; or b) registering the location of signals from the fluorescent marker acquired in step 1 with the location of signals from the fluorescent marker acquired in step 2, and (i) generating an initial image of at least part of the sample from the detected fluorescent signals; and (ii) selecting a region of interest from the initial image, and detecting by fluorescence, signals from at least the first binder and the fluorescent marker to generate the first image at a higher resolution than the initial image.