Disclosed herein are scientific instrument support systems, as well as related methods, apparatus, computing devices, and computer-readable media. Some embodiments provide a scientific instrument including detectors supporting one or more spectroscopic modalities and an imaging modality and further including an electronic controller configured to process streams of measurements received from the detectors. The electronic controller operates to generate a base image of the sample based on the measurements corresponding to the imaging modality and further operates to generate an anomaly map of the sample based on the base image and further based on differences between measured and autoencoder-reconstructed spectra corresponding to different pixels of the base image. In at least some instances, the anomaly map can beneficially be used in a quality-control procedure to identify, within seconds, specific problem spots in the sample for more-detailed inspection and/or analyses.