Abstract
Depth-dependent fluence-compensation in photoacoustic (PA) imaging is paramount for accurate quantification of chromophores from deep tissues. Here we present a user-friendly toolkit named PHANTOM (PHotoacoustic ANnotation TOolkit for MATLAB) that includes a graphical interface and assists in the segmentation of ultrasound-guided PA images. We modelled the light source configuration with Monte Carlo eXtreme and utilized 3D segmented tissues from ultrasound to generate fluence maps to depth compensate PA images. The methodology was used to analyze PA images of phantoms with varying blood oxygenation and results were validated with oxygen electrode measurements. Two preclinical models, a subcutaneous tumor and a calcified placenta, were imaged and fluence-compensated using the PHANTOM toolkit and the results were verified with immunohistochemistry. The PHANTOM toolkit provides scripts and auxiliary functions to enable biomedical researchers not specialized in optical imaging to apply fluence correction to PA images, enhancing accessibility of quantitative PAI for researchers in various fields.