Investigating respiratory rhythm generation using endoscopic 2-photon and photoacoustic imaging
Breathing is a continuous oscillatory activity, driven by a complex neuronal network deep in the brain. Core
to this network are intermingled neuronal microcircuits that generate the respiratory rhythm, yet we still
lack fundamental understanding about how it works in adults in vivo. Our aim is to image the activity of
these microcircuits with cellular resolution, to identify activity patterns that could underlie respiratory
rhythm generation. Yet, the depth of these neurons prevents the use of conventional high resolution
imaging techniques. We recently developed a flexible lensless endoscope that is compatible with non-linear
imaging, therefore enabling 2-photon imaging deep in the brain of freely behaving animals. We are also
developing a photoacoustic imaging setup, to image non-invasively in deep soft tissue, which will be tested
in parallel. Using both systems, we will image the neurons of different respiratory rhythm generating
microcircuits, based on their neurochemical phenotype and their projection patterns.
Deep neuronal circuits imaging; respiratory rhythm generation; lensless 2-photon endoscope; functional
micro-network dynamics; photoacoustic imaging.
Our objective is to image with cellular resolution neuronal microcircuits involved in respiratory rhythm
generation in freely moving animals. The successful applicant will (i) perform stereotaxic injections of
viruses for expression of calcium indicators in respiratory neuronal groups in adult mice and rats, (ii) implant
the lensless endoscope (for 2-photon imaging) or the Fabry-Perot polymer film (for photoacoustic imaging),
and (iii) image neuronal activity simultaneously with recordings of respiratory activity.
We are looking for a highly motivated candidate with a PhD in neuroscience, biophysics, or similar.
Independence and a strong interest in technological development are essential. Previous experience in
rodent surgery, electrophysiology, signal processing and programming are required. Previous experience
with stereotaxic injection of viruses, calcium imaging, optogenetics, and working in the field of central
respiratory control would be a plus but is not compulsory.
In the case of an existing project, please explain the links between the two projects (5 lines)
It is not the continuation of an existing project.
2 to 5 references related to the project
- Del Negro CA, Funk GD, Feldman JL, “Breathing matters”, Nat. Rev. Neurosci., 2018 Jun;19(6):351-367,
- Ramirez JM and Baertsch NA, “The dynamic basis of respiratory rhythm generation: one breath at a
time”, Annu. Rev. Neurosci., 41, 475-499, 2018, DOI: 10.1146/annurev-neuro-080317-061756.
- G. Meng et al., “High-throughput synapse-resolving two-photon fluorescence microendoscopy for deepbrain
volumetric imaging in vivo,” eLife, vol. 8, p. e40805, Jan. 2019, DOI: 10.7554/eLife.40805.
- E. Zhang, J. Laufer, and P. Beard, “Backward-mode multiwavelength photoacoustic scanner using a
planar Fabry-Perot polymer film ultrasound sensor for high-resolution three-dimensional imaging of
biological tissues,” Appl. Opt., AO, vol. 47, no. 4, pp. 561–577, 2008, DOI: 10.1364/AO.47.000561.
- X. L. Deán-Ben et al., “Functional optoacoustic neuro-tomography for scalable whole-brain monitoring of
calcium indicators,” Light: Science & Applications, vol. 5, no. 12, p. e16201, 2016, DOI:
3 main publications from each PI over the last 5 years
Clément Menuet (lead supervisor)
 Menuet C, Connelly AA, Bassi JK, Melo MR, Le S, Kamar J, Kumar NN, McDougall SJ, McMullan S, Allen
AM. PreBötzinger complex neurons drive respiratory modulation of blood pressure and heart rate. Elife
2020 Jun 15 ;9e57288. DOI: 10.7554/eLife.57288.
 Menuet C, Le S, Dempsey B, Connelly AA, Kamar J, Jancovski N, Bassi JK, Walters K, Simms AE, Hammond
A, Fong AY, Goodchild AK, McMullan S, Allen AM. Excessive respiratory modulation of blood pressure
triggers hypertension. Cell Metabolism 2017 Mar 7;25(3):739-748. DOI: 10.1016/j.cmet.2017.01.019.
 Ngo HB, Melo MR, Layfield S, Connelly AA, Bassi JK, Xie L, Menuet C, McDougall SJ, Bathgate RAD, Allen
AM. A chemogenetic tool that enables functional neural circuit analysis. Cell Reports 2020 Sep
15;32(11):108139. DOI: 10.1016/j.celrep.2020.108139.
Hervé Rigneault (co-supervisor 1)
 V. Tsvirkun, S. Sivankutty, K. Baudelle, R. Habert, G. Bouwmans, O. Vanvincq, E. R. Andresen, and H.
Rigneault, "Flexible lensless endoscope with a conformationally invariant multi-core fiber," Optica 6, 1185-
1189 (2019). https://doi.org/10.1364/OPTICA.6.001185
 S. Sivankutty, V. Tsvirkun, O. Vanvincq, G. Bouwmans, E. R. Andresen, and H. Rigneault, "Nonlinear
imaging through a Fermat’s golden spiral multicore fiber," Optics Letters 43, 3638-3641 (2018).
 Esben Ravn Andresen, Siddharth Sivankutty, Viktor Tsvirkun, Géraud Bouwmans, Hervé Rigneault,
‘Ultrathin endoscopes based on multicore fibers and adaptive optics: a status review and perspectives,’ J.
Biomed. Opt. 21(12), 121506 (2016). https://doi.org/10.1117/1.JBO.21.12.121506
Thomas Chaigne (co-supervisor 2)
 Schulze L, Henninger J, Kadobianskyi M, Chaigne T, Faustino AI, Hakiy N, Albadri S, Schuelke M, Maler L,
Del Bene F, Judkewitz B. Transparent Danionella translucida as a genetically tractable vertebrate brain
model. Nat Methods. 2018 Nov;15(11):977-983. doi: 10.1038/s41592-018-0144-6.
 Chaigne T, Arnal B, Vilov S, Bossy E, Katz O. Super-resolution photoacoustic imaging via flow-induced
absorption fluctuations. Optica, 4(11), 1397-1404 (2017) doi: 10.1364/OPTICA.4.001397
 Chaigne T, Gateau J, Allain M, Katz O, Gigan S, Sentenac A, Bossy E. Super-resolution photoacoustic
fluctuation imaging with multiple speckle illumination. Optica, 3(1), 54-57 (2016) doi: