Alpha-particle therapy offers a potential advantage in cancer treatment because the short-range (50-80µm) and high local energy deposition of alpha particles is adaptable to precise target selection and efficient tumor elimination. Safe and effective clinical use requires quantitative tools to visualize and characterize the spatial dose deposition of treatment radiation in targeted and nontargeted cells for accurate dosimetry of treatment regimens. This study demonstrates a procedural toolkit that may be used in conjunction with an ionizing-radiation quantum imaging detector (iQID) camera to image and analyze event-by-event alpha particle deposition in tissues. We propose intensity-based computer vision methods to co-register sectioned images for dose analysis and provide a procedure to quantify dose in a sample using a Monte Carlo dose kernel. Finally, we fuse dose map images with HE-stained microscope images to address the impact of histology factors on dose uptake.