The real-time and spatially-resolved detection and identification of analytes in biological media present important goals for next-generation nanoscale probes and sensors. To this end, we employ the intrinsic near-infrared fluorescence of single-walled carbon nanotubes which is photostable yet sensitive to the immediate environment. Analyte identification is achieved by modulation of the nanotube’s spectral response, resulting in distinct optical fingerprints. We transiently map the nanotube emission responses spatially in live cells and tissues, facilitating unprecedented bioanalytical measurements.