Schaefer lab | Connectomics: Representation of spatial odour signals in projection neurons

A 2023 Crick PhD project with Andreas Schaefer
Deadline for applications has passed.

Key information

Applications closed
10 November 2022, 12:00 GMT
Posted 05 October 2022

Research topics

Background texture taken from the lab imagery.

A 2023 Crick PhD project with Andreas Schaefer

Project background and description

The Sensory Circuits and Neurotechnology Group aims to decipher how circuits in the brain represent, encode, and process information. We use sensory systems in mice as a model system and a variety of techniques – from synchrotron x-ray tomography and volume electron microscopy to identify neural circuits, in vivo imaging in behaving animals, electrophysiology in vivo and in vitro, optogenetics, molecular tools, to computational and theoretical approaches. Furthermore, we are actively involved in developing technology especially in the realm of large-scale electrophysiology and x-ray tomography.

The aim of this specific project is to decipher the functional anatomy of information processing in the olfactory bulb. In this connectomics approach you will combine in vivo multiphoton functional imaging of odour-evoked signals with synchrotron X-ray tomography (parallel-beam and nano-holotomography) and / or volume electron microscopy (serial blockface scanning electron microscopy). The specific goal is to delineate how projection neurons of the olfactory bulb encode sensory information about space, in particular how projection neurons belonging to the same input channel (glomerulus / olfactory receptor class) process and represent information about the olfactory world differentially. 

Candidate background 

The successful candidate will either come from a degree in neuroscience / biology with an exceptionally strong background and interest in mathematics / data science approaches. 

Alternatively, the successful candidate will come from a degree in engineering / physics / mathematics / material science and have strong background and strong interest in and enthusiasm for experimental neuroscience / neurophysiology. 

Extensive quantitative, analytical ability will be essential and experience in computer programming (ideally Python or Matlab or similar) and enthusiasm for advanced data analysis approaches will be highly advantageous. 

The project will build on our recent work developing histological techniques, electron microscopy and sycnhrtron X-ray tomography as well as performing in vivo multiphoton imaging experiments in awake mice. Thus, the project offers broad traingin in experimental physiological and anatomical technique as well as data analysis and processing approaches.

This is a highly collaborative project and ability and enthusiasm to work and communicate in a team is absolutely essential. You will work closely with senior scientists in the lab, imaging specialists, computational neuroscientists, the EM core facility, as well as synchrotron X-ray physicists. 


1.         Ackels, T., Erskine, A., Dasgupta, D., Marin, A.C., Warner, T.P.A., Tootoonian, S., . . . Schaefer, A.T. (2021)

            Fast odour dynamics are encoded in the olfactory system and guide behaviour.

            Nature 593: 558-563. PubMed abstract

2.         Bosch, C., Ackels, T., Pacureanu, A., Zhang, Y., Peddie, C.J., Berning, M., . . . Schaefer, A.T. (2022)

            Functional and multiscale 3D structural investigation of brain tissue through correlative in vivo physiology, synchrotron microtomography and volume electron microscopy.

            Nature Communications 13: 2923. PubMed abstract

3.         Dasgupta, D., Warner, T.P.A., Erskine, A. and Schaefer, A.T. (2022)

            Coupling of mouse olfactory bulb projection neurons to fluctuating odor pulses.

            Journal of Neuroscience 42: 4278-4296. PubMed abstract

4.         Tootoonian, S., Schaefer, A.T. and Latham, P.E. (2022)

            Sparse connectivity for MAP inference in linear models using sister mitral cells.

            PLOS Computational Biology 18: e1009808. PubMed abstract

5.         Zhang, Y., Ackels, T., Pacureanu, A., Zdora, M.C., Bonnin, A., Schaefer, A.T. and Bosch, C. (2022)

            Sample preparation and warping accuracy for correlative multimodal imaging in the mouse olfactory bulb using 2-photon, synchrotron X-ray and volume electron microscopy.

            Frontiers in Cell and Developmental Biology 10: 880696. PubMed abstract