Challenges and advances in optical 3D mesoscale imaging

Munck, Sebastian and Cawthorne, Christopher and Escamilla‐Ayala, Abril and Kerstens, Axelle and Gabarre, Sergio and Wesencraft, Katrina and Battistella, Eliana and Craig, Rebecca and Reynaud, Emmanuel G. and Swoger, Jim and McConnell, Gail (2022) Challenges and advances in optical 3D mesoscale imaging. Journal of Microscopy, 286 (3). pp. 201-219. ISSN 0022-2720 (

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Optical mesoscale imaging is a rapidly developing field that allows the visualisation of larger samples than is possible with standard light microscopy, and fills a gap between cell and organism resolution. It spans from advanced fluorescence imaging of micrometric cell clusters to centimetre-size complete organisms. However, with larger volume specimens, new problems arise. Imaging deeper into tissues at high resolution poses challenges ranging from optical distortions to shadowing from opaque structures. This manuscript discusses the latest developments in mesoscale imaging and highlights limitations, namely labelling, clearing, absorption, scattering, and also sample handling. We then focus on approaches that seek to turn mesoscale imaging into a more quantitative technique, analogous to quantitative tomography in medical imaging, highlighting a future role for digital and physical phantoms as well as artificial intelligence.