<p>Plant growth and development strongly depend on the uptake of soil minerals and their distribution within plants. Various electrophysiological techniques have been developed to study these ion transport processes and the role of ions in signal transduction pathways. An important non-invasive method is provided by Scanning Ion-Selective Electrodes (SISE), which are used to detect ion fluxes. These SISE-measurements depend on software that coordinates the continuous electrode movement between two positions, as well as data collection and analysis. We developed two LabView-based programs; the SISE-Monitor and SISE-Analyser that enable ion flux recordings and their analysis, respectively. These applications are freely available, both as windows-executable files that enable routine measurements, as well as the LabView source code that allows insights into the routines used for measurement and analysis. Moreover, the source code can be used to develop new functions, such as the combined measurement of extracellular ion fluxes with SISE and cellular ion concentrations with fluorescent dyes, or proteins.</p>