20 21 throughout the 1940s 1 and 1950s 2 when post-mortem and resected human lung tissues were 55 routinely available. These pioneering studies have strongly influenced our current understanding 56 of the spectrum of tuberculous lesions, morphology and pathology. 57The prevailing dogma in the TB field is that TB granulomas form spherical or ovoid 58 structures within the parenchyma 3-11 . However, this assumption is not always supported by 59 experimental evidence. Further, remarkably little is known about the structure of the caseous 60 granuloma, the distinctive feature of infection by Mtb in humans. Hence, a deeper understanding 61 of the human TB granuloma is urgently needed to more accurately inform preventive and 62 therapeutic TB strategies. 63The ability to examine pathological TB structures within large tissues in 3D could allow 64 identification of disease-specific features and improve diagnosis. Hence, it is reasonable to 65 speculate that the limitations of conventional histological analysis have begun to hinder more 66 detailed examination of human TB pathophysiology in the current antibiotic era, especially with the 67 emergence of HIV. Other factors contributing to our limited understanding are the reliance on 68 animal models which do not recapitulate human pulmonary TB phenotypes, and the paucity of 69 routinely available resected human TB lung tissues 12,13 . Therefore, imaging approaches that 70 provide high-resolution digital 3D imaging of TB lesions will allow comprehensive analysis of the 71 complex 3D microanatomical features specific to pulmonary TB. 72 X-ray computed tomography (CT) is an invaluable imaging tool for nondestructive 73 assessment of tissue in medical diagnosis [14][15][16] . High resolution micro-CT (µCT) is typically used 74 for materials with high electron density and lends itself to ex vivo analysis of pathologies involving 75 bone structure or calcium deposition 17 . Imaging of soft tissue can be improved by addition of 76 electron-dense contrast agents (e.g., iodine, osmium, or tungsten) or using high-energy flux 77 monochromatic x-rays generated by synchrotrons. To our knowledge, however, no study has 78 reported the use of µCT to examine bacterial or viral disease in human lungs. While µCT is an 79 experimental imaging modality, high-resolution computed X-ray tomography (HRCT) is often used While conventional histopathological analysis provides detailed information on very small areas of 130 interest, it cannot contextualize TB lesions within the overall lung architecture. This has limited our 131 understanding of the distribution and shapes of lesions within the human TB lung. µCT has the 132 potential to improve our understanding of the evolution of granuloma formation and structure, 133 relative to the diffusion of drugs, O 2 and nutrients. To contextualize TB lesions relative to the 134 vasculature and airways, we used µCT to scan a large slice (~14 x 1.5 x 6 cm) of infected lung at 135 52.0 µm resolution (Figure 2A, Figure S1, Video S1). 3D segmentation shows th...