An ImageJ plugin for ion beam imaging and data processing at AIFIRA facility

Abstract Quantification and imaging of chemical elements at the cellular level requires the use of a combination of techniques such as micro-PIXE, micro-RBS, STIM, secondary electron imaging associated with optical and fluorescence microscopy techniques employed prior to irradiation. Such a numerous set of methods generates an important amount of data per experiment. Typically for each acquisition the following data has to be processed: chemical map for each element present with a concentration above the detection limit, density and backscattered maps, mean and local spectra corresponding to relevant region of interest such as whole cell, intracellular compartment, or nanoparticles. These operations are time consuming, repetitive and as such could be source of errors in data manipulation. In order to optimize data processing, we have developed a new tool for batch data processing and imaging. This tool has been developed as a plugin for ImageJ, a versatile software for image processing that is suitable for the treatment of basic IBA data operations. Because ImageJ is written in Java, the plugin can be used under Linux, Mas OS X and Windows in both 32-bits and 64-bits modes, which may interest developers working on open-access ion beam facilities like AIFIRA. The main features of this plugin are presented here: listfile processing, spectroscopic imaging, local information extraction, quantitative density maps and database management using OMERO.