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Optical Microscopy : principles and applications in Neurosciences

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M2_E04_OpticalMicroscopy Planning2021.pdf

Biology Master, ENS
Bio-M2_E04 | Optical Microscopy
Year and Semester : M2 S1
Duration : 2 weeks, 60 hours | 30h course - 30h practicals
First and last day of class : November 15th -26th, 2021
Hours : 9am-12pm | 2pm-5pm
Maximum class size : 12-16 students


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 and wave optics is required (image formation with a lens, wave propagation and the principles of interference and diffraction,..). An upgrade in optics (principles of image formation in microscopy, notions of resolution, optical sectioning, imaging in scattering tissue) will be carried out during the first day of the course.
Maths : easy manipulation 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 hands-on sessions, the aim of this course is to teach basic and advanced techniques in neuronal imaging and their application in neuroscience.
Themes : Basics of optical microscopy | Optogenetical tools in neuroscience | 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 a microscope and basics of laser optics. Then the lectures will cover a range of classical and advanced techniques in microscopy and their applications in neurosciences. 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 paper.
It will take place the last day of the course. It consists in an oral presentation of about 30 minutes.

Teaching team

Laurent Bourdieu (ENS, Paris)
Stephane Dieudonné (ENS, Paris)
Vincent Villette (ENS, Paris)
Cathie Ventalon ENS, Paris)
Willy Supatto (Ecole Polytechnique, Palaiseau)
Anatole Chessel (Ecole Polytechnique, Palaiseau)
Thomas Deneux (NeuroPsi, Saclay)
Isabelle Ferezou (NeuroPsi, Saclay)
Gaël Moneron (Institut Pasteur)
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

• 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.