Loading Events

« All Events

  • This event has passed.

Thesis defense – Agata Idziak

7 November 2022 / 15:00

CGFB and on zoom (https://u-bordeaux-fr.zoom.us/j/6325485773)

Defense in english

Thesis Supervisor : Valentin Nägerl (IINS)


Investigating the structure and function of brain extracellular space using super-resolution microscopy


Every cell in the brain is embedded in a fluid called the extracellular space (ECS). Its structural complexity with intercellular gaps as narrow as ten nanometers, presents a challenge of visualizing the ECS in living brain tissue. Our recently established SUSHI technique overpasses this issue enabling to image the ECS with a nanoscale resolution. During my PhD training, I unveiled new structural information about ECS, as well as characterized novel tools to study it. My PhD work was divided into three projects, all aiming at investigating the structure and function of brain ECS.
(1) Using the SUSHI approach, I studied the heterogeneity of ECS structure across hippocampal layers, which are known to have a very distinct cellular organization. My results show that ECS varies in volume and width across hippocampus, raising a question whether region-based differences in ECS structure in the hippocampus could support the unique anatomical as well as functional properties of each layer.
(2) Chemical fixation leads to drastic shrinkage of ECS, yet it was only investigated in a context of electron microscopy. With help of SUSHI, I performed a systematic analysis of the impact of chemical fixation on brain tissue morphology. The results revealed only minor structural alteration, meaning that chemical fixation alone is not the reason for such dramatic effects.
(3) Studying calcium signals in the ECS was a challenge since all available biosensors were not designed to measure ion concentrations with a millimolar affinity. Here, I characterized a novel tool, GreenT, to capture extracellular calcium dynamics. By imaging GreenT signals during electrophysiological stimulations, I was able to measure calcium fluctuations in the ECS upon neuronal activation. This is the beginning of applying this tool for physiology studies aiming at understanding the role of extracellular calcium.

Keywords: super-resolution STED microscopy, SUSHI, ECS, chemical fixation, extracellular calcium, GreenT


Dembitskaya Y, Boyce A, Idziak A, (…), Nägerl V.U. Shadow imaging as a versatile method for panoptic visualization of living brain tissue. In preparation.

Grassi D, Idziak A, Lee A, Calaresu I, Sibarita JB, Cognet L, Nägerl V.U., Groc L. Nanoscale and functional heterogeneity of the hippocampal extracellular space. Under revision.

Idziak A, Inavalli Krishna VVG, Bancelin S, Arizono M, Nägerl V.U. Super-resolution analysis of the effects of chemical fixation on the cellular microarchitechture of organotypic mouse brain slices. In preparation.

Arizono M, Idziak A, Quici F, Nägerl V.U. Getting sharper: the brain under the spotlight of super-resolution microscopy (2022). Trends in Cell Biology. 1851:1-14.

Arizono M, (…), Idziak A, (…), Nägerl V.U. Nanoscale imaging of the functional anatomy of the brain (2021). De Gruyter. https://doi.org/10.1515/nf-2021-0004.

Arizono M, Idziak A, Nägerl V.U. Il faut être trois pour danser le tango Illuminer les signaux Ca2+ des synapses tripartites (2021). Med Sci. 37: 127–129.

Antoniou A, Khudayberdiev S, Idziak A, Jacob R, Bicker S, Schratt G. The dynamic membrane recruitment of miRNA processing complexes in neurons controls dendritogenesis (2017). EMBO Reports. e44853.


MARSICANO Giovanni, directeur de Recherche, INSERM (president)
TØNNESEN Jan, Associate Professor, Achurraco Bilbao (reviewer)
IMIG Cordelia, Associate Professor, University of Copenhagen (reviewer)
HRABĚTOVÁ Sabina, Associate Professor, SUNY, (examiner)

I subscribe to the newsletter:


7 November 2022
Event Category: