Accepted Article Perspectives, potentials and trends of ex vivo and in vivo optical molecular pathology Christoph Krafft* 1 , Ferdinand von Eggeling 1,2,3,4 , Orlando Guntinas-Lichius 3 , Arndt Hartmann 5 , Maximilian J. Waldner 6 , Markus F. Neurath 6 , and Jürgen Popp 1,2,4 1. Leibniz Institute of Photonic Technology, Albert-Einstein-Str. 9, 07745 Jena, Germany 2. Institute of Physical Chemistry and Abbe Center of Photonics, University Jena, Germany 3. Department of Otorhinolaryngology, University Hospital Jena, Germany 4. Jena Biophotonic and Imaging Laboratory, DFG Core Facility, 07745 Jena, Germany 5. Institute of Pathology, University Erlangen-Nürnberg, Germany 6. Department of Medicine 1, University Hospital Erlangen-Nürnberg, Germany Key words: Hyperspectral imaging, photoacoustic tomography, molecular endoscopy, nonlinear optical imaging 1. Optical molecular pathology A number of optical techniques have been suggested for applications in molecular pathology, intraoperative diagnosis and endoscopy. Modern trends in biophotonics for clinical diagnosis and therapy to solve unmet clinical needs were recently summarized [1]. Table 1 gives an overview of their current state in head and neck cancer which can be transferred in a similar way to other pathologies. Next, the photonic approaches are briefly described. Autofluorescence of tissue is the natural emission of light by biomolecules when they have absorbed light [2]. Most common autofluorophores are NADPH, NADH (excitation 340 nm, fluorescence 450 nm) and flavins (excitation 380-490 nm, fluorescence 520-560 nm). It can be applied ex vivo, in vivo without artificially added fluorescent markers and is already licensed for clinical use. Tumor tissue is usually associated with reduced autofluorescence. However, as autofluorescence can be quenched by numerous processes, this method lacks specificity. Specificity can be improved by labels or contrast media which is utilized in induced fluorescence, confocal laser endomicroscopy and near infrared It is pivotal for medical applications, such as non-invasive histopathologic characterization of tissue, to realize label- free and molecule-specific representation of morphologic and biochemical composition in real-time with subcellular spatial resolution. This unmet clinical need requires new approaches for rapid and reliable real-time assessment of pathologies to complement established diagnostic tools. Photonic imaging combined with digitalization offers the potential to provide the clinician the requested information both under in vivo and ex vivo conditions. This report summarizes photonic approaches and their use in combination with image processing, machine learning and augmented virtual reality might to solve current challenges in modern medicine. Details are given for pathology, intraoperative diagnosis in head and neck cancer and endoscopic diagnosis in gastroenterology. Multimodal image of a colon section combining CARS, SHG and TPEF for label-free contrast of the crypt structure. This article is protected by copyright. All rights reserved. This article has been accepted for publication and undergone full peer review but has not been through the copyediting, typesetting, pagination and proofreading process, which may lead to differences between this version and the Version of Record. Please cite this article as doi: 10.1002/jbio.201700236