Computational Spectral Microscopy (CSM)

Our work in the optical and mechanical design of computational spectral imagers has been targeted towards fluorescence microscopy applications. We have been involved with the design of both a pushbroom system (SmacM) and a snapshot system (MacSim). The pushbroom system is based on a static aperture coded single disperser design that is translated in order to capture a 3D cube (2D spatial, 1D spectral). The snapshot system, however, is a dual disperser architecture which uses advanced signal processing techniques (compressive sensing) to measure a 3D cube in a snapshot.

Scanning multiplex aperture coded microscopy (SmacM)

SmacM evolved as an extension to our high throughput aperture coded spectrometer designs for Raman chemometrics. A high throughput aperture coded spectrometer is placed at the intermediate image plane of a microscope. The spectrometer is scanned perpendicular to its dispersion direction. Scanning the spectrometer creates a 3D cube (2D spatial, 1D spectral) of any given scene placed at the object plane to the microscope. Compared to a conventional pushbroom system, the aperture coded system has 32 times greater throughput.


Two systems were designed: the first design had a spectrometer placed at the intermediate image plane of a lab built microscope housed in a rapid-protyped case. The second design consisted of an aperture coded spectrometer placed at the intermediate image plane of an upright research-grade microscope (Zeiss Axioplan 2). The spectral resolution of both aperture coded spectrometers is about 1nm over the range of 550nm-665nm. The spatial resolution for both system designs differ. The first design is limited by the 10x Nikon objective used which yields a 5.4 micron spatial resolution. The second design is limited by the coupling optics and the various Zeiss objectives used yielding a spatial resolution range from 7.7 microns to 1.54 microns. We have proof-of-concept datacube results with a monochromatic and bichromatic illuminated chrome on quartz mask 'DISP'. Thus far, experimental results have been extended towards reconstructions made with fixed-cellular assays. A future goal invovles extending this technology to biologically relevant microscopy-based applications.


  1. (Peer Review) Gehm, M.E., Kim, M., Fernandez, C. , and Brady, D. "High-throughput, multiplexed pushbroom hyperspectral microscopy," Optics Express
  2. Gehm, M.E. and Brady, D.J., High-throughput hyperspectral microscopy, Proceedings of SPIE - The International Society for Optical Engineering, vol. 6090 (2006), pp. 609007-, San Jose, CA, United States [12.644828]

Multispectral aperture coded snapshot imaging microscope (MacSim)

MacSim is based on a dual disperser optical architecture which using compressive sensing signal processing techniques in order to measure a 3D data cube (2D spatial, 1D spectral) in a snapshot.

MacSim can measure over thirty spectral channels over the spectral range of 450nm-750nm. The spectral resolution of MacSim is about 10nm. The goal of MacSim is to produce a datacube in a single snapshot. Our application of interest includes imaging dynamic cellular events and fixed cellular assays for fluorescence microscopy applications.


  1. M.E. Gehm, R. John, D.J. Brady, R.M. Willet, and T.J. Schulz,, "Single-shot compressive espectral imaging with a dual-disperser architecture," Opt. Express 15, 14013-14027 (2007)