Challenges and advances in optical 3D mesoscale imaging

Sebastian Munck*, Christopher Cawthorne, Abril Escamilla‐Ayala, Axelle Kerstens, Sergio Gabarre, Katrina Wesencraft, Eliana Battistella, Rebecca Craig, Emmanuel G. Reynaud, Jim Swoger, Gail McConnell

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

10 Citations (Scopus)
95 Downloads (Pure)


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.

Original languageEnglish
Pages (from-to)201-219
Number of pages19
JournalJournal of Microscopy
Issue number3
Early online date23 Apr 2022
Publication statusPublished - Jun 2022


  • scattering
  • 3D imaging
  • absorption
  • clearing
  • light sheet microscopy
  • Mesolens
  • mesoscale
  • optical projection tomography


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