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New radiotherapy techniques such as Intra-Operative Radiotherapy use low energy photons to provide effective treatment of diseases such as Breast Cancer by simultaneously reducing treatment costs and time consumed, while preserving healthy tissue in patients. Although studies are being conducted to compare the effects of low energy photons used in Intra-Operative Radiotherapy with the high-energy photons used in External Beam Radiotherapy, much information regarding the differences in the biological effect of these two clinical modalities of treatment is not available. The development of novel modes of super-resolution microscopy such as Spectral Precision Distance Microscopy (SPDM_phymod) allows detection of changes taking place within the cells based on the behaviour of chromatin rearrangement, using histone proteins that have been tagged by conventional Green Fluorescent Proteins. This research study is aimed at utilizing the superior optical resolution capability of the SPDM_phymod setup to detect and quantify changes taking place in the nuclei of HeLa cells after irradiating with a low energy (50kV) photon beam and a high energy (6MV) photon beam at different incubation times post irradiation. The study of conformational changes in the chromatin material will allow investigation into the repair mechanisms taking place in the cells at different times as the cell tries to cope with the damage induced by the radiation. HeLa cells were irradiated using a low-energy photon beam from the INTRABEAM™ machine and a high-energy photon beam from a conventional Linear Accelerator. After incubating for 15 minutes, 30 minutes, 12 hours and 48 hours; the irradiated cells were imaged using the SPDM_phymod microscope. Reconstruction of the images allowed successful localization of individual histone proteins within the nucleus. An algorithm was then used to analyse changes in the clustering of histone proteins in these cells. The results of the cluster analysis revealed distinct patterns of clustering in the cells irradiated from both machines. 15 minutes after radiation, the cells irradiated by the high-energy photons exhibited 13% of histone clustering which linearly increased with incubation to 25%. On the other hand, cells irradiated with low-energy photons displayed 20% of clustering after 15 minutes that reduced to 14% after 48 hours while following a non-linear pattern of increase and subsequent decrease. These observations suggest that discrete biological effects take place in cells irradiated from both machines, which also varies with the time allowed for repair. Additional analysis of the heterochromatin and euchromatin regions, along with co-localization studies of irradiation-induced foci stained with γH2AX antibodies would allow further exploration of global changes taking place in the chromatin after irradiation from the two machines and contribute to the understanding of what exactly happens in the nuclei of cells after exposure to radiation. The results from this study may also lead to the development of a new approach to biological dosimetry.