Summary We describe an open‐source freeware programme for high throughput analysis of nanoSIMS (nanometre‐scale secondary ion mass spectrometry) data. The programme implements basic data processing and analytical functions, including display and drift‐corrected accumulation of scanned planes, interactive and semi‐automated definition of regions of interest (ROIs), and export of the ROIs' elemental and isotopic composition in graphical and text‐based formats. Additionally, the programme offers new functions that were custom‐designed to address the needs of environmental microbiologists. Specifically, it allows manual and automated classification of ROIs based on the information that is derived either from the nanoSIMS dataset itself (e.g. from labelling achieved by halogen in situ hybridization) or is provided externally (e.g. as a fluorescence in situ hybridization image). Moreover, by implementing post‐processing routines coupled to built‐in statistical tools, the programme allows rapid synthesis and comparative analysis of results from many different datasets. Af
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