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Background. Availability of open tools is a key feature to facilitate the development of pre-clinical research of Magnetic Resonance-guided High Intensity Focused Ultrasound (MR-HIFU). MatMRI is a toolbox that allows direct communication with a Philips{trade mark, serif} MRI scanner in a Matlab{trade mark, serif} environment, which is well-known in many laboratories. MatMRI performs real-time acquisition of magnitude and phase images that can be processed to estimate changes of temperature. Available functionality of MatMRI includes acquisition of individual slices and volumetric data. Analogously to MatMRI, MatHIFU is a toolbox for the control of the Philips Sonalleve MR-HIFU system. MatHIFU allows the execution of user-defined treatment protocols such as thermal ablation, hyperthermia or drug delivery. MatMRI and MatHIFU can be used independently or in combination. Methods. MatMRI was based on the official tool for MRI data-dumping made by Philips Healthcare. Multi-threading capabilities were added to maximize real-time processing performance. Basic use of MatMRI involves four basic steps: initiate communication, subscribe to MRI data, query for new images and unsubscribe. If required, MatMRI can also pause/resume the scanning and update on real-time the location and orientation of the images. MatHIFU performs the execution of sonication protocols and allows real-time monitoring. Basic use of MatHIFU requires also four steps: preparation of sonication protocol, initiate communication, execute sonication protocol and monitor the state of execution. Results. MatMRI was integrated into existing software used to control a table designed for animal experimentation (FUS Instruments, Canada). The integration in the existing software was seamless and delivered real-time estimation of changes of temperature in a mouse model. Using MatHIFU and MatMRI, a complete new interface to control the Sonalleve system was developed to perform in vivo experiments allowing adapted conditions for the experimental model. Conclusions. MatMRI and MatHIFU leverage considerably the existing MRI and MR-HIFU platforms to conduct pre-clinical research. MatMRI simplifies considerably the efforts required to perform real-time measurements of MR data and its possibilities are beyond thermal applications. MatHIFU facilitates the exploration of new therapeutic applications using the Philips MR-HIFU Sonalleve system. Both matMRI and matHIFU are aimed to be freely available to other research groups under coordination of Philips Healthcare. [ABSTRACT FROM AUTHOR]