We report on novel hyper-spectral imaging filter-modules based on acousto-optic tuneable filters (AOTF). The AOTF functions as a full-field tuneable bandpass filter which offers fast continuous or random access tuning with high filtering efficiency. Due to the diffractive nature of the device, the unfiltered zero-order and the filtered first-order images are geometrically separated. The modules developed exploit this feature to simultaneously route both the transmitted whitelight image and the filtered fluorescence image to two separate cameras. Incorporation of prisms in the optical paths and careful design of the relay optics in the filter module have overcome a number of aberrations inherent to imaging through AOTFs, leading to excellent spatial resolution. A number of practical uses of this technique, both for in vivo auto-fluorescence endoscopy and in vitro fluorescence microscopy were demonstrated. We describe the operational principle and design of recently improved prototype instruments for fluorescence-based diagnostics and demonstrate their performance by presenting challenging hyper-spectral fluorescence imaging applications.