Imagerie à grande vitesse de cellules vivantes, de la microscopie à la nanoscopie, grâce à la détection neuromorphique // High speed Live cell imaging from microscopy to nanoscopy thanks to event-based detection

State of the art: : Fluorescence microscopy is a key technic to observe biological questions with a high specificity, which still triggers major developments to improve spatial resolution but also the acquisition speed to match live cell imaging constraints. New approaches have been developed to bypass the diffraction limit based on structuration of the excitation (Structured illumination SIM) or by controlling the emission of the fluorescent emitters (single molecule localization : SMLM) which allows to reach nanometer scale. However current implementations mainly incorporate classical cameras which constraints the acquisition speed. Within the project we propose to implement new detection strategy based on event camera, which offers a continuous acquisition which not only permit to increase the acquisition speed but also open new optical implementation for live cell imaging from microscopy to nanoscopy. NanoBio team is at the forefront for the development of new optical concepts for both microscopy and nanoscopy, and in particular to improve 3D imaging by introducing an original patented structured excitation (Nat. Photonics 2015,20211,2, Nat. Commun. 20193). Abbelight, a French SME founded in 2016, focuses on the development of super-resolution add-on transforming inverted microscopes into nanoscopes.
While single-molecule localization microscopy (SMLM) provides high spatial resolution, the acquisition time needed to localize molecules can limit its ability to capture fast, dynamic events. Yet, biological processes, such as protein trafficking, membrane dynamics, and organelle movement, often occur on timescales exceeding the temporal resolution of SMLM, but is also still challenging for conventional diffraction limited imaging leading to blurred or inaccurate image reconstructions. Event-based cameras widely used to track displacement in industrial applications, has become compatible with fluorescence microscopy thanks to new generation of sensors. This event camera offers a continuous observation of the sample, but only return event following intensity change, for example associated to cell movement. By only monitoring changes, ultimate speed can be reached, but this also open completely new avenues to conceive the optical microscope and nanoscope.
Objectives and Methodology: With our synergistic approach, we are aiming at addressing existing challenges in acquisition speed and 3D resolution, to enable observations of live cell processes at various scales of resolution down to nanoscopic precision. Benefiting from the competitive research environment of supervisors, and the training and network provided by LIGHTinPARIS, the PhD candidate will be central for the development of pioneering instrument combining optical and image processing innovations for key biological questions.
• Event camera based detection will be combined with various implementation of structured excitation to improve spatial resolution down to a factor 2, while pushing the temporal resolution capability. A second step, will be to combine with single molecule localization, where the event based detection not only allow to push further the speed for live samples, but also to permit demodulation of the fluorescence induced by the structured excitation to reach nearly isotropic resolution.
• Alternative processing with deep learning algorithms : by returning events only during variation of intensities either due to movement or induce by a controlled modulated excitation, new workflow of processing based on deep learning will also allow us to push further the needed signal to noise ratio and increase the acquisition speed.
• Applications : these new optical implementations will be fully characterized before addressing biological questions with close collaborators in biology, to decipher live cell dynamics mechano-sensible mechanisms at the nanoscale which steers cancer cell migration.
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State of the art: : Fluorescence microscopy is a key technic to observe biological questions with a high specificity, which still triggers major developments to improve spatial resolution but also the acquisition speed to match live cell imaging constraints. New approaches have been developed to bypass the diffraction limit based on structuration of the excitation (Structured illumination SIM) or by controlling the emission of the fluorescent emitters (single molecule localization : SMLM) which allows to reach nanometer scale. However current implementations mainly incorporate classical cameras which constraints the acquisition speed. Within the project we propose to implement new detection strategy based on event camera, which offers a continuous acquisition which not only permit to increase the acquisition speed but also open new optical implementation for live cell imaging from microscopy to nanoscopy. NanoBio team is at the forefront for the development of new optical concepts for both microscopy and nanoscopy, and in particular to improve 3D imaging by introducing an original patented structured excitation (Nat. Photonics 2015,20211,2, Nat. Commun. 20193). Abbelight, a French SME founded in 2016, focuses on the development of super-resolution add-on transforming inverted microscopes into nanoscopes.
While single-molecule localization microscopy (SMLM) provides high spatial resolution, the acquisition time needed to localize molecules can limit its ability to capture fast, dynamic events. Yet, biological processes, such as protein trafficking, membrane dynamics, and organelle movement, often occur on timescales exceeding the temporal resolution of SMLM, but is also still challenging for conventional diffraction limited imaging leading to blurred or inaccurate image reconstructions. Event-based cameras widely used to track displacement in industrial applications, has become compatible with fluorescence microscopy thanks to new generation of sensors. This event camera offers a continuous observation of the sample, but only return event following intensity change, for example associated to cell movement. By only monitoring changes, ultimate speed can be reached, but this also open completely new avenues to conceive the optical microscope and nanoscope.
Objectives and Methodology: With our synergistic approach, we are aiming at addressing existing challenges in acquisition speed and 3D resolution, to enable observations of live cell processes at various scales of resolution down to nanoscopic precision. Benefiting from the competitive research environment of supervisors, and the training and network provided by LIGHTinPARIS, the PhD candidate will be central for the development of pioneering instrument combining optical and image processing innovations for key biological questions.
• Event camera based detection will be combined with various implementation of structured excitation to improve spatial resolution down to a factor 2, while pushing the temporal resolution capability. A second step, will be to combine with single molecule localization, where the event based detection not only allow to push further the speed for live samples, but also to permit demodulation of the fluorescence induced by the structured excitation to reach nearly isotropic resolution.
• Alternative processing with deep learning algorithms : by returning events only during variation of intensities either due to movement or induce by a controlled modulated excitation, new workflow of processing based on deep learning will also allow us to push further the needed signal to noise ratio and increase the acquisition speed.
• Applications : these new optical implementations will be fully characterized before addressing biological questions with close collaborators in biology, to decipher live cell dynamics mechano-sensible mechanisms at the nanoscale which steers cancer cell migration.
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Début de la thèse : 01/10/2025

Programme COFUND LIGHTinPARIS

Université Paris-Saclay GS Physique

572 Ondes et Matière

-connaissances en optique -connaissances en deep learning -intéressé(e) par le developpement instrumental -connaissance en python -intéressé(e) par le travail interdisciplinaire
-knowledge in optics -interested in instrumental development -knowledge in python -knowledge in deep learning -interested in interdisciplinary work