Charged particle therapy (CPT) is an advanced modality of radiation therapy which has grown rapidly worldwide, driven by recent developments in technology and methods of delivery. To ensure safe and high quality treatments, various instruments are used for a range of different measurements such as for quality assurance, monitoring and dosimetry purposes. With the emergence of new and enhanced delivery techniques, systems with improved capabilities are needed to exceed existing performance limitations of conventional tools. The Medipix3 is a hybrid pixel detector able to count individual protons with millisecond time resolution at clinical flux with near instant readout and count rate linearity. The system has previously demonstrated use in medical and other applications, showing wide versatility and potential for particle therapy. In this work we present measurements of the Medipix3 detector in the 60 MeV ocular proton therapy beamline at the Clatterbridge Cancer Centre, UK. The beam current and lateral beam profiles were evaluated at multiple positions in the treatment line and compared with EBT3 Gafchromic film. The recorded count rate linearity and temporal analysis of the beam structure was measured with Medipix3 across the full range of available beam intensities, up to $3.12 times 10^{10}$ protons/s. We explore the capacity of Medipix3 to provide non-reference measurements and its applicability as a tool for dosimetry and beam monitoring for CPT. This is the first known time the performance of the Medipix3 detector technology has been tested within a clinical, high proton flux environment.
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