We developed a near-infrared small animal imaging system, IR VIVO, that provides real-time images, videos and spectral imaging in the NIR-I and shortwave infrared (SWIR or NIR-II) regions. We found that SWIR wavelengths can give optimal resolution for in vivo optical imaging of deep organs in mice up to 3 cm due to the low tissue autofluorescence, scattering and absorption of light at these wavelengths. We also showed how this higher penetration depth can enable the detection of small wavelength changes in the emission of carbon nanotube-based sensors implanted in vivo using a continuously tunable filter.First, we demonstrated superior image clarity and penetration depth at NIR-II wavelengths (1000-1700 nm) in vivo using an FDA approved dye, indocyanine green (ICG) in a mouse. We used 780 nm excitation, detection using a Zephir 1.7 InGaAs camera and 1250 nm long-pass emission filter. We found low tissue autofluorescence at 1250 nm. The ICG dye imaging resulted in superior visualization of microvasculature, perfusion, measurement of hearst rate, respiratory rate, hepatobiliary and intestinal contractions. Further anatomical and functional imaging was carried out by looking at the kinetics of ICG, resulting in the identification of different organs.Second, In vivo near-infrared hyperspectral imaging of carbon nanotubes was conducted using a continuously-tunable filter in the imager. A diffraction volume Bragg grating (VBG), was used to provide narrow-band wavelength selection. Coupled with a homogeneous global illumination, spectrally-defined images were acquired in the entire field of view. The result was a dataset containing both 2D spatial information and the full spectrum for each point in the image. We conducted near-infrared hyperspectral imaging of single-walled carbon nanotubes to measure small wavelength changes of the nanotubes implanted into live mice. Hyperspectral measurements of carbon nanotube sensors for lipids in the liver as well as implantable sensors for doxorubicin were conducted, facilitating liver disease monitoring and drug pharmacokinetics measurements.Finally, we believe wide-area NIR-II imaging and spectral/hyperspectral measurements have broad potential applications for the use of carbon nanotubes and other NIR-I/II materials in basic materials/biology, translational, and clinical work, including sensor arrays, point-of-care measurements, implants, whole small animal imaging and intraoperative/surgical imaging.