Measuring physics inside cells
Quantitative imaging methods that turn microscopy into measurement — from two-photon FRAP and FLIM to physics-informed deep learning.
Understanding cellular mechanisms often requires imaging that does more than show: it has to measure physical quantities — diffusion coefficients, protein–protein interactions through fluorescence lifetime, local density. I have developed and applied such methods for over twenty years, first as a PhD student and then at the Institut Curie imaging facility (PICT-IBiSA), across dozens of collaborative projects in cell biology — endosome biogenesis, membrane trafficking, mechanotransduction, nuclear-pore biology.
Highlights include:
- the first two-photon FRAP analysis of cytoskeletal proteins in intact microvilli;
- FLIM/FRET instrumentation for protein interactions in living cells;
- image-correlation methods for molecular mobility in complex systems, and FRAP inside biofilms;
- co-supervision of Philippe Roudot’s PhD on lifetime estimation for moving objects in frequency-domain FLIM;
- most recently, a physics-informed neural network that recovers quantitative phase — and hence intracellular density — from a single brightfield image.
Key outputs
- Waharte F., et al. A two-photon FRAP analysis of the cytoskeleton dynamics in the microvilli of intestinal cells. Biophys. J. 88 (2005). doi:10.1529/biophysj.104.049619
- Coscoy S., Waharte F., et al. Molecular analysis of microscopic ezrin dynamics by two-photon FRAP. PNAS 99 (2002). doi:10.1073/pnas.192084599
- Waharte F., et al. Diffusion measurements inside biofilms by image-based FRAP with a commercial confocal microscope. Appl. Environ. Microbiol. 76 (2010). doi:10.1128/AEM.00754-10
- Roudot P., Kervrann C., Blouin C.M., Waharte F. Lifetime estimation of moving subcellular objects in frequency-domain FLIM. J. Opt. Soc. Am. A 32 (2015). doi:10.1364/JOSAA.32.001821
- Chenouard N., et al. Objective comparison of particle tracking methods. Nature Methods 11 (2014). doi:10.1038/nmeth.2808