Methods to localize cell specific alterations within the 3D context of the lung

The lung is a heterogeneous organ, composed of morphologically different sub-compartments. When analyzing lung pathologies, it is important to collect the spatial location of lesions, to allow the translation of e.g. preclinical study results to the human lung, or the formulation of targeted treatment strategies. For the purpose of this review, bronchopulmonary dysplasia will serve as an example for a lung pathology to be studied, but the methods demonstrated can be adapted to other pathologies as well. The review's focus will lie on common histological methods and the potential to use them for both the study of cellular features and location assessment. Morphological characteristics, as well as intracellular states related to cell cycle and cell death will be considered. In an advanced section, the combination of multiple imaging methods into analysis pipelines is detailed, describing different combinatorial possibilities with their advantages and use in the research context. Through the integration of microscopy and computed tomography into one process, it is possible to assess both 3D location and cellular features, with the option of employing immunohistochemical markers for the detection of specific proteins as well. This is a tool that can be used in addressing both transitional and longitudinal research questions regarding lung pathologies.