Spectral microscopy has the ability to generate a large volume of data in a short period of time. Unfortunately, commercial software has been limited in its ability to handle batch data. I developed a suite of MATLAB scripts called SpectralMagic that address these problems. SpectralMagic leverages the power of Bio-Formats to provide a wealth of microscope metadata. Images are automagically processed with parallelized spectral unmixing algorithms based on their unique metadata attributes. The batch functionality of the software allows users to click-and-walk-away. You can even configure the scripts to send a text message when your data is ready.

I released the SpectralMagic scripts during the 2014 Physiology course at the Marine Biological Laboratory. The students used the software to analyze hundreds of gigabytes of spectral images, including the 100GB spectral z-stacks shown below. The video displays a focus-through of a spectral z-stack where each color represents a different bacterial taxon. As of this writing, SpectralMagic is still used for routine analysis by the Borisy Lab at The Forsyth Institute and the Phillips Lab at Caltech.

Spectral z-stack processed using SpectralMagic. Image credits: Bryan Weinstein, Lishibanya Mohapatra, and Matti Gralka