Cornell Spectrum Imager: Open Source Spectrum Analysis with ImageJ

Here we present a free, open-source software tool for spectral analysis of electron energy loss (EELS), energy dispersive x-ray (EDX), or cathodoluminescence (CL) data the Cornell Spectrum Imager (CSI) (Fig. 1) [1]. Spectral imaging, whether via EELS, EDX or CL, is a powerful approach to analyzing materials in a wide array of fields [2]. Proper analysis of spectral data requires software for extracting the chemical signatures present in a spectrum. Basic analysis requires background extrapolation, background subtraction, and signal integration [3]. However, the commercial software available for spectrum analysis remains an expensive, complicated, and time-consuming black box. Worse, licensing terms generally restrict the software to a single computer tied to the dataacquisition microscope or a handful of machines. For user facilities, educational institutes, or any other setting where multiple users on a single tool can be expected, the limited availability of software becomes the bottleneck to data analysis, user training, and throughput. Faced with several hundred users logging over 10,000 hours on our instruments at Cornell, we decided to write a universal data analysis tool that could be freely distributed, would run on all computers, and in order to minimize training, would present the same user interface for imaging, EELS and EDX data analysis. Our goal was software that could be run with minimal instruction or training this meant ensuring all options needed for basic analysis were immediately visible to the user, and also limiting those options to avoid overwhelming a new user.