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Optical Microscopy : principles and applications

Master in Life Sciences, ENS
BIO_M2_E04 | Optical Microscopy : principles and applications
Year and Semester : M2 | S1
Duration : 2 weeks, 60 hours | 30h course - 30h practicals
Dates : November 11-22, 2024
Maximum class size : 12-14 students

—2024-2025 programme to come—


Stéphane Dieudonné, Biology Department, ENS
Laurent Bourdieu, Biology Department, ENS
Olivier Collin, Biology Department, ENS
Andréa Dumoulin, Biology Department, ENS




Optical microscopy | Structural imaging | Functional imaging | Optogenetics.

Course prerequisites

Optics : Some basic knowledge in geometrical optics is required (image formation with a lens,..). An upgrade in optics (principles of image formation, resolution and optical sectioning in microscopy) will be carried out during the first day of the course.
Maths : use of integrals, derivatives, complex numbers. An upgrade in Fourier analysis will be proposed the first day.

Course objectives and description

Aims : Through theoretical courses and practical sessions, the aim of this course is to teach basic and advanced techniques in biological imaging. The course will focus mainly on imaging techniques applied to large-scale tissues and whole organisms, and on their application in neurosciences and developmental biology.
Themes : Basics of optical microscopy | Optogenetical tools | Super resolution optical microscopy | Light sheet microscopy | Two-photon microscopy | In vivo optogenetics | Imaging in freely behaving animals | Mesoscopic functional imaging | Data analysis in functional imaging | Image analysis | Connectomics
Organization : The course is organized in lectures and hands-on workshops. An upgrade in optics will be carried out during the first day of the course. It will be followed by two days of practical work on two different optical bench setups to study image formation in microscopy and basics of laser optics. The lectures will then cover a range of classical and advanced techniques in microscopy and their applications in biology. During the next two days, the students will follow workshops on setups in research labs and directly related to the lectures (super-resolution, light-sheet imaging, two-photon imaging).


Assessment will be made on the basis of a critical analysis of a research article. It will take place the last day of the course and consists in an oral presentation of about 30 minutes.

Teaching team

Laurent Bourdieu (ENS, Paris)
Stéphane Dieudonné (ENS, Paris)
Vincent Villette (ENS, Paris)
Cathie Ventalon (ENS, Paris)
Willy Supatto (Ecole Polytechnique, Palaiseau)
Anatole Chessel (Ecole Polytechnique, Palaiseau)
Sébastien Wolf (ENS, Paris)
Isabelle Ferezou (NeuroPsi, Saclay)
Guillaume Dupuis (ISMO, Université Paris Saclay)
Emiliano Ronzitti (Institut de la Vision, Paris)
Brice Bathelier (Institut de l’Audition, Paris)
Nicolas Renier (ICM, Paris)

Suggested readings in relation with the module content

Review articles
• Lecoq J, Orlova N, Grewe BF. Wide. Fast. Deep : Recent Advances in Multiphoton Microscopy of In Vivo Neuronal Activity. J Neurosci. 2019 Nov 13 ;39(46):9042-9052. doi : 10.1523/JNEUROSCI.1527-18.2019. Epub 2019 Oct 2. PMID : 31578235 ; PMCID : PMC6855689.
• Yang W, Yuste R. In vivo imaging of neural activity. Nat Methods. 2017 Apr ;14(4):349-359. doi : 10.1038/nmeth.4230. Epub 2017 Mar 31. PMID : 28362436 ; PMCID : PMC5903578.
• Ntziachristos V. Going deeper than microscopy : the optical imaging frontier in biology. Nat Methods. 2010 Aug ;7(8):603-14. doi : 10.1038/nmeth.1483. Epub 2010 Jul 30. PMID : 20676081.
• Packer AM, Roska B, Häusser M. Targeting neurons and photons for optogenetics. Nat Neurosci. 2013 Jul ;16(7):805-15. doi : 10.1038/nn.3427. Epub 2013 Jun 25. PMID : 23799473 ; PMCID : PMC4928704.
• Chen IW, Papagiakoumou E, Emiliani V. Towards circuit optogenetics. Curr Opin Neurobiol. 2018 Jun ;50:179-189. doi : 10.1016/j.conb.2018.03.008. Epub 2018 Apr 7. PMID : 29635216 ; PMCID : PMC6027648.

• "Optique - Fondements et applications" José-Philippe Pérez, Éric Anterrieu. Dunod, EAN. 9782100807833.
This is a very complete educational book that covers all the basic concepts of geometrical and wave optics. It also describes the Fourier transform. A good book for the basics of optics.
• "Ondes lumineuses : Propagation, optique de Fourier, cohérence", de Jean-René Champeau, Renaud Carpentier, Ivan Lorgeré. (EAN : 978-2804158897 ; ISBN : 2804158896).
A very complete educational book. Chapters 1 to 6 can be consulted to find the principles of geometrical optics, the notion of progressive wave, the phenomenon of diffraction, the resolution of optical instruments...
• "Fundamentals of Photonics" de Bahaa E. A. Saleh et Malvin Carl Teich. (ISBN-10 ‏ :‎ 9780471839651 ; ISBN-13 ‏ : ‎978-0471839651).
A very clear book. Typically, one should look at chapters 1,2,4,5, and appendix A.

To go further, the reference book In optical microscopy is the following :
• "Introduction to Optical Microscopy" 2nd Edition by Jerome Mertz. ASIN : B07VBNQFY1.