Selected Work & Short Descriptions

• 2019
  P. Roudot, W. R. Legant, K. M. Dean, A. F David, D. W. Gerlich, R. Fiolka, E. Betzig, and G. Danuser. U-Track 3D: A Tracking Framework to Quantify, Observe and Contextualize Intracellular Dynamics in Three Dimensions. In Preparation.
  Light-sheet microscopy enables 3D imaging of dynamic sub-cellular processes in the full cellular volume and away from any hard surfaces. However, complex dynamics and structural overlaps challenge the interpretation and validation of the data. In this work, we adapt 3D volume to the human eye by estimating thin regions of interest that follows biological processes over time. Because the dataset are too large to be validated entirely, we propose an unsupervised estimator for 3D measurement uncertainty. With this method, we revealed and quantified previously unobservable interactions such as chromosome capture and 3D adhesion mechanisms.

  A. F. David, P. Roudot, W. R. Legant, E. Betzig, G. Danuser, and D. W. Gerlich. . Augmin accumulation on long-lived microtubules drives amplification and kinetochore-directed growth. Journal of Cell Biology.
  PDF In this work, we apply the u-track 3D framework to interrogate mitosis robustness with three-dimensional Lattice Light-sheet microscopy. The unsupervised estimation of multiple dynamic region of interest inside the mitotic spindle revealed a systematic bias of microtubules toward chromosomes. We could measure that augmin-mediated, non-centrosomal, nucleation provide a structurally induced mechanism for fast and error-free chromosome segregation.

• 2017
  P. Roudot, L. Ding, K. Jaqaman, C. Kervrann, and G. Danuser. Piecewise-Stationary Motion Modeling and Iterative Smoothing to Track Heterogeneous Particle Motions in Dense Environments. IEEE Transactions on Image Processing. PDF The study of dynamic processes is challenged by the limited temporal sampling of fluorescence microscopy. Chemically triggered motions often result in the imaging of unpredictably large displacements. We designed an efficient stochastic smoothing algorithm using past and future time-point to recover fast transitions that can not be predicted by conventional approaches.

• 2016
  P. Roudot*, K. M. Dean*, C. R. Reis, E. S. Welf, M. Mettlen, and R. Fiolka. Diagonally Scanned Light-Sheet Microscopy for Fast Volumetric Imaging of Adherent Cells. Biophysical Journal. * denotes equal contribution. PDF
  How to define "fast" ? In this paper we propose a new light-sheet microscope design reaching 4Hz volumetric frequency. We prove through mathematic modeling , experimental measures and simulations that this frequency is sufficient to measure speed up to 4 micron/s in the diffusive case and 8 micron/s in a directed case. We also show that 3Hz is enough for the accuracy at the membrane, but that 4Hz must be reached to measuer accurate dynamics in the area the golgy apparatus. This is one way we can define "fast" in light-sheet microscopy.

• 2015
  P. Roudot, C. Kervrann, C. M. Blouin, and F. Waharte. Lifetime Estimation of Moving Subcellular Objects in Frequency-Domain Fluorescence Lifetime Imaging Microscopy. Journal of the Optical Society of America A. PDF Nanosecond-scale fluorescence decay is a powerful metric for the transfer of energy and interaction between fluorescently-labeled molecules in fixed cells. We designed a joint estimator of fluorescence lifetime, structural motion and microscope parameter to apply this technique to non-invasive live cell experiments.

Research experience

• 2014/07 - present
  Human Frontier Postdoctoral Fellow at UT Southwestern Medical Center (TX, U.S.A.) advised by Pr Gaudenz Danuser. Unsupervised discovery of intracellular processes through quantitative 3D microscopy.

• 2014/01 - 2014/03
  Visiting student at Institut Curie (France) hosted by Pr. Jean Salamero.
  FRET efficiency analysis on dynamical caveolin structure in Frequency domain FLIM.

• 2012/11 - 2013/02 Visiting student at Harvard Medical School (MA, U.S.A.) hosted by Pr. Gaudenz Danuser.
  Heterogeneous motion estimation of multiple particles in dense condition.

• 2010/10 - 2013/12
  Ph.D. student at Inria Rennes (France) advised by Pr. Charles Kervrann (Inria) and Dr. François Waharte (Institut Curie). Lifetime estimation of moving vesicles in frequency-domain fluorescence lifetime imaging.

Complete List of Peer-Reviewed Publications & Patents

• 2019
  P. Roudot, W. R. Legant, K. M. Dean, A. F David, D. W. Gerlich, R. Fiolka, E. Betzig, and G. Danuser. U-Track 3D: A Tracking Framework to Quantify, Observe and Contextualize Intracellular Dynamics in Three Dimensions. In Preparation.

  A. Mihai, J. Noh, M. J. Sandi, P. Roudot, R. Rottapel, G. Danuser, and K. M. Hahn. Novel Biosensor Design Reveals the Role and Regulation of GEF-H1 in Cell Migration. Submitted in Journal of Cell Biology.

  A. F. David, P. Roudot, W. R. Legant, E. Betzig, G. Danuser, and D. W. Gerlich. Augmin-Mediated Amplification of Long-Lived Spindle Microtubules Directs plus-Ends towards Kinetochores. Under review in Journal of Cell Biology.

  B. Chang, M. Kittisopikul, K. M. Dean, P. Roudot, E. S. Welf, and R. P. Fiolka. Universal Light-Sheet Generation with Field Synthesis. In press in Nature Methods.

• 2018
  A. Lakoduk, P. Roudot, M. Mettlen, H. M. Grossman, P.-H. Chen, and S. L. Schmid. Mutant P53 Triggers a Dynamin-1/APPL1 Endosome Feedback Loop That Regulates B1 Integrin Recycling and Migration. BioArxiv. Under review in Journal of Cell Biology.

  A. S. Mohan, K. M. Dean, S. Y. Kasitinon, T. Isogai, V. S. Murali, S. J. Han, P. Roudot, A. Groisman, E. Welf, and G. Danuser. Hyperactive Rac1 Drives MAPK-Independent Proliferation in Melanoma by Assembly of a Mechanosensitive Dendritic Actin Network. BioRxiv. Under revision.

  S. Manandhar, P. Bouthemy, E. Welf, P. Roudot, and C. Kervrann. A Sparse-to-Dense Method for 3D Optical Flow Estimation in 3D Light-Microscopy Image Sequences. Proc. IEEE Int. Symp. on Biomedical Imaging (ISBI’18).

• 2017
  P. Roudot, L. Ding, K. Jaqaman, C. Kervrann, and G. Danuser. Piecewise-Stationary Motion Modeling and Iterative Smoothing to Track Heterogeneous Particle Motions in Dense Environments. IEEE Transactions on Image Processing.

  K. M. Dean, P. Roudot, E. S. Welf, T. Pohlkamp, G. Garrelts, J. Herz, and R. Fiolka. Imaging Subcellular Dynamics with Fast and Light-Efficient Volumetrically Parallelized Microscopy. Optica.

• 2016
  P. Roudot*, K. M. Dean*, C. R. Reis, E. S. Welf, M. Mettlen, and R. Fiolka. Diagonally Scanned Light-Sheet Microscopy for Fast Volumetric Imaging of Adherent Cells. Biophysical Journal. * denotes equal contribution.

• 2015
  K. M. Dean, P. Roudot, E. S. Welf, G. Danuser, and R. Fiolka. Deconvolution-Free Subcellular Imaging with Axially Swept Light Sheet Microscopy. Biophysical Journal.

  P. Roudot, C. Kervrann, C. M. Blouin, and F. Waharte. Lifetime Estimation of Moving Subcellular Objects in Frequency-Domain Fluorescence Lifetime Imaging Microscopy. Journal of the Optical Society of America A.

• 2014
  P. Roudot Image Processing Methods for Dynamical Intracellular Processes Analysis in Quantitative Fluorescence Microscopy. Thesis, University of Rennes 1.

  C. Kervrann, P. Roudot, and F. Waharte. Approximate Bayesian Computation, Stochastic Algorithms and Non-Local Means for Complex Noise Models. In IEEE International Conference on Image Processing (ICIP 14).

• 2013
  N. Chenouard, I. Smal, F. de Chaumont, M. Maska, I. F. Sbalzarini, G. Yuanhao, J. Cardinale, C. Carthel, S. Coraluppi, M. Winter, A. R. Cohen, W. J. Godinez, K. Rohr, Y. Kalaidzidis, L. Liang, J. Duncan, H. Shen, Y. Xu, K. Magnusson, J. Jaldén, P. Paul-Gilloteaux, P. Roudot, C. Kervrann, F. Waharte, J.-Y. Tinevez, J. Willemse, K. Celler, H.-W. Dan, Y.-S. Tsai, C. Ortiz de Solórzano, J.-C. Olivo-Marin, and E. Meijering, An Objective Comparison of Particle Tracking Methods Nature Methods, 2013.

  P. Roudot, C. Kervrann, J. Boulanger, F. Waharte. Noise modeling for intensified camera in fluorescence imaging: application to image denoising. Proc. IEEE Int. Symp. on Biomedical Imaging (ISBI’13), San Francisco, April 2013.

• 2012
  P. Roudot, C. Kervrann, J. Boulanger, F. Waharte. Lifetime map reconstruction in frequency-domain fluorescence lifetime imaging microscopy. Proc. IEEE Int. Conf. on Image Processing (ICIP’12), Orlando, Florida, October 2012.

  P. Roudot, C. Kervrann, F. Waharte. Lifetime estimation of moving vesicles in frequency-domain fluorescence lifetime imaging microscopy. Proc. IEEE Int. Symp. on Biomedical Imaging (ISBI’12), Barcelona, Spain, May 2012.

• 2011
  P. Roudot, S. Baudry, F. Lefebvre, A. Robert. Method for H264 selective encryption Technicolor Patent. February 2011.