Publications

PhD Theses

  • Gwendal Fouché. Immersive and Interactive Visualization of Temporal 3D Data, INSA Rennes, Dec 2022 (language: english)
  • Jiayi Hong. Machine Learning Supported Interactive Visualization of HYBRID 3D and 2D Data for the Example of Plant Cell Lineage Specification. Université Paris-Saclay, Feb 2023 (language: english)
  • Manuel Petit. Mapping Tools and Methods to Scale Quantitative Analysis of Temporal Time-Lapse Series from Individual to Population of Plant Organs. École normale supérieure de Lyon (ENS-L), May 2023 (language: english)

Preprints and submissions

  • Hong, J. Maciejewski, R., Trubuil, A., Isenberg, T. Comparative visualization of machine learning predictions to improve human-AI teaming on the example of cell lineage. IEEE Transactions on Visualization and Computer Graphics, 2023 (under review)

Academic Journals

2023
  • Fouché, G., Argelaguet, F., Faure, E., Kervrann, C. Immersive and interactive visualization of 3D spatiotemporal data using a space time hypercube: application to cell division and morphogenesis analysis, Frontiers in Bioinformatics, 2023. (accepted)
  • Prigent, S., Nguyen, H.-H., Leconte, L., Valades-Cruz, C.A., Hajj, B., Salamero, J. Kervrann, C. SPITFIRe: a supermaneuverable algorithm for fast denoising and deconvolution of 3D fluorescence microscopy images and videos, Nat. Scientific Reports, 13(1): 1489, 2023.
  • Prigent, S., Dutertre, S., Bidaud-Meynard, A., Bertolin, G., Michaux, G., Kervrann, C. Sparse denoising and adaptive estimation enhances the resolution and contrast of fluorescence emission difference microscopy based on array detector, Optics Letters, 48(4): 847–919, 2023.
2022
  • Blanc, T., Verdier, H., Regnier, L., Planchon, G., Guérinot, C., el Beheiry, M., et al. Towards human in the loop analysis of complex point clouds: Advanced visualizations, quantifications, and communication features in virtual reality. Frontiers in Bioinformatics, 1, 1., 2022.
  • Guérinot, C., Marcon, V., Godard, C., Blanc, T., Verdier, H., Planchon, G., et al. New approach to accelerated image annotation by leveraging virtual reality and cloud computing. Frontiers in Bioinformatics, 1., 2022.
  • Kar, A., Petit, M., Refahi, Y., Cerutti, G., Godin, C., Traas, J. Benchmarking of deep learning algorithms for 3D instance segmentation of confocal image datasets. PLoS Comput. Biol.,18(4):e1009879, 2022.
  • Prigent, S., Valades-Cruz, C.A., Leconte, L., Salamero, J., Kervrann, C. STracking: a free and open-source Python library for particle tracking and analysis,Bioinformatics, btac65, 2022.
  • Prigent, S., Dutertre, S., Bidaud-Meynard, A., Bertolin, G., Michaux, G., Kervrann, C. Sparse denoising and adaptive estimation enhances the resolution and contrast of fluorescence emission difference microscopy based on array detector, Optics Letters, 48(4): 847–919, 2023.
  • Prigent, S., Valades-Cruz, C.A., Leconte, L., Maury, L., Salamero, J., Kervrann, C. BioImageIT: Open-source framework for integration of image data-management with analysis, Nat. Methods, 2022.
  • Sereno, M., Gosset, S., Besançon, L., Isenberg, T. HYBRID touch/tangible spatial selection in augmented reality. Comput. Graph. Forum, 41(3):403–415, 2022.
  • Sereno, M., Wang, X., Besançon, L., McGuffin, M. J., Isenberg, T. Collaborative work in augmented reality: A survey. IEEE Transactions on Visualization and Computer Graphics. 28 :2530–2549, 2022.
  • Valades-Cruz, C.A., Leconte, L., Fouché, G., Blanc, T., van Hille, N., Fournier, K., Tao, L., Gallean, B., Deslandes, F., Hajj, B., Faure, E., Argelaguet, F., Trubuil, A., Isenberg, T., Masson, J.-B., Salamero, J., Kervrann, C. Challenges of intracellular visualization using virtual and augmented reality, Frontiers in Bioinformatics, 2022.
2020
  • Beheiry, M., Godard, C., Caporal, C., Marcon, V., Ostertag, C., Sliti, O., et al. Diva: Natural navigation inside 3D images using virtual reality. J. Mol. Biol., 432:4745–4749, 2020.
  • Blanc, T., el Beheiry, M., Caporal, C., Masson, J.-B., and Hajj, B. Genuage: Visualize and analyze multidimensional single-molecule point cloud data in virtual reality. Nat. Methods, 17:1100–1102, 2020.
  • Manandhar, S., Bouthemy, P., Welf, E., Danuser, G., Roudot, P., Kervrann, C. 3D flow field estimation and assessment for live cell fluorescence microscopy, Bioinformatics, 36(5):13171325, 2020.
2019
  • Briane, V., Vimond, M., Valades Cruz, C.A., Salomon, A, Wunder, C., Kervrann, C. A sequential algorithm to detect diffusion switching along intracellular particle trajectories,Bioinformatics, btz489,  2019.
2018

Peer-reviewed Conference Articles

2022
  • G. Fouché, F. Argelaguet, E. Faure, C. Kervrann. Timeline design space for immersive exploration of time-varying spatial 3D data. 10.48550/arXiv.2206.09910, Proc. ACM Symp. on Virtual Reality Software and Technology (VRST ’22), Tsukuba, Japan, 2022, pp. 1–11.
  • J. Hong, A. Trubuil, T. Isenberg. LineageD: An Interactive visual system for plant cell lineage assignments based on correctable machine learning. Proc. Computer Graphics Forum 41.3, Jun 2022, pp. 195–207.
  • Petit, G. Cerutti, C. Godin, G. Malandain. Robust plant cell tracking in fluorescence microscopy 3D+T series. Proc. Int. Symp. Biomedical Imaging (ISBI), Kolkata, India, Mar 2022, pp. 1–4.
  • E.A.D. Santos, J. Hong, T. Isenberg. A design space for linked 2D and 3D visual representations. Posters at the IEEE Conference on Visualization, Proc. IEEE Conf. on Visualization (IEEE VIS), Oklahoma City, USA, Oct 2022.
2021
  • A. Badoual, M. Arizono, A. Denizot, M. Ducros, H. Berry, V. Nägerl, C. Kervrann. Simulation of astrocytic calcium dynamics in Lattice Light Sheet Microscopy images. Proc IEEE Int. Symp. Biomedical Imaging (ISBI), Nice, France, Apr 2021, pp. 135–139.
  • J. Hong, F. Argelaguet, A. Trubuil, T. Isenberg. Design and evaluation of three selection techniques for tightly packed 3D objects in cell lineage specification in botany. Proc. Graphics Interface (GI), (virtually in) Vancouver, BC, Canada, Mississauga, ON, Canada, May 2021, pp. 213–223.
2020
  • J. Hong, F. Argelaguet, A. Trubuil, T. Isenberg. An interactive system for analyzing plant embryo cell division. Proc. IEEE Conf. on Visualization (IEEE VIS), (poster), (virtually in, poster), Salt Lake City, Utah, Oct 2020.
  • S. Manandhar, P. Bouthemy, E. Welf, P. Roudot, C. Kervrann. 3D optical flow estimation combining 3D Census signature and total variation regularization. Proc. IEEE Int. Symp.  Biomedical Imaging (ISBI), Iowa City, USA, Apr 2020, pp. 965–968.
  • A. Salomon, C.A. Valades-Cruz, L. Leconte, C. Kervrann. Dense mapping of intracellular diffusion and drift from single particle tracking data analysis. Proc IEEE Int. Conf.  Acoustics, Speech and Signal Processing (ICASSP), Barcelona, Spain, May 2020. pp. 966–970.
2018
  • S. Manandhar, P. Bouthemy, E. Welf, P. Roudot, 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), Washington, Apr 2018, pp. 952–956.

Other communications

2021
  • A. Badoual. Simulation of astrocytic calcium signals in microscopy images based on kinetic models, online Symp. on “Spatiotemporal Encoding and Decoding in Cell Signaling”, organized by the Multi-Organization Thematic, Cell Biology, Development and Evolution (ITMO – BCDE), March 18, 2021.
  • S. Prigent, C. A. Valades-Cruz, L. Leconte, J. Salamero, C. Kervrann. SPITFIR(e): a supermaneuverable image restoration algorithm for 2D, 3D and 3D+Time microscopy images, BioImage Informatics, Paris, France, Nov 2021. (poster)
2020
  • G. Fouché, F. Argelaguet, E. Faure, C. Kervrann, MorphoNet VR: Visualization of 3D Temporal Light-Sheet Microscopy Imagery in VR, NEUBIAS Network of EUropean BioImage Analysts Conference, Bordeaux, France, Feb 2020.
  • L. Leconte, C.A. Valades-Cruz, C. Kervrann, J. Salamero,Virtual 12th light sheet fluorescence microscopy conference, 2020.
  • S. Prigent, C. Kervrann, J. Salamero, BioImage-IT: Design data analysis workflows using tools from different languages and keep track of the metadata, Network of BioImage Analysts (NEUBIAS), Bordeaux Feb 2020
  • S. Prigent, C. Kervrann, J. Salamero, BioImage-IT,Quantitative BioImaging (QBI), Oxford, UK, Jan 2020.
  • A. Salomon, C. Kervrann, Precise mapping of intracellular diffusion and drift from SPT data analysis,Quantitative BioImaging (QBI), Oxford, UK, Jan 2020.
  • C.A. Valades-Cruz, L. Leconte, C. Wunder, C. Kervrann, L. Johannes, J. Salamero, 3D tracking of endocytic and exocytic events using lattice light sheet microscopy,Quantitative BioImaging (QBI), Oxford, UK, Jan 2020.
2019
  • S. Manandhar, P. Bouthemy, P. Roudot, C. Kervrann, 3D motion estimation in 3D light microscopy image sequences: application to cell migration, Quantitative BioImaging (QBI), Rennes, France, Jan 2019.
  • A. Salomon, V. Briane, M. Vimond, C.A. Vlades-Cruz, C. Kervrann, Analyzing and quantifying intracellular particles movements in 3D LLSM data,Quantitative BioImaging (QBI), Rennes, France, Jan 2019.
  • A. Valades-Cruz, A. Forrester, C. Wunder, C. Kervrann, J. Salamero, L. Johannes, 3D tracking of endocytic events using lattice light sheet microscopy,Quantitative BioImaging (QBI), Rennes, France, Jan 2019.

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