Jean-Christophe Olivo-Marin

Orcid: 0000-0001-6796-0696

Affiliations:
  • Institut Pasteur, Paris, France


According to our database1, Jean-Christophe Olivo-Marin authored at least 136 papers between 1993 and 2024.

Collaborative distances:
  • Dijkstra number2 of four.
  • Erdős number3 of four.

Awards

IEEE Fellow

IEEE Fellow 2012, "For contributions to image analysis and its applications in biological imaging".

Timeline

Legend:

Book 
In proceedings 
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PhD thesis 
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Links

Online presence:

On csauthors.net:

Bibliography

2024
Deep ContourFlow: Advancing Active Contours with Deep Learning.
CoRR, 2024

Scribble-based fast weak-supervision and interactive corrections for segmenting whole slide images.
CoRR, 2024

Motion Classification Based on Geometrical Features of Trajectories.
Proceedings of the IEEE International Symposium on Biomedical Imaging, 2024

Particle Tracking in Biological Images with Optical-Flow Enhanced Kalman Filtering.
Proceedings of the IEEE International Symposium on Biomedical Imaging, 2024

Semi-Supervised Segmentation with Topological Penalization for Quantifying Retinal Degeneration in Histological Sections.
Proceedings of the IEEE International Symposium on Biomedical Imaging, 2024

Wavelet-Based Sparse Non-Negative Matrix Factorization for Bioluminescent Imaging Unmixing.
Proceedings of the IEEE International Symposium on Biomedical Imaging, 2024

2023
From Nano to Macro: An overview of the IEEE Bio Image and Signal Processing Technical Committee.
IEEE Signal Process. Mag., June, 2023

Reformulating Optical Flow to Solve Image-Based Inverse Problems and Quantify Uncertainty.
IEEE Trans. Pattern Anal. Mach. Intell., May, 2023

Domain Adapted Multitask Learning for Segmenting Amoeboid Cells in Microscopy.
IEEE Trans. Medical Imaging, 2023

Tracking Intermittent Particles with Self-Learned Visual Features.
Proceedings of the 20th IEEE International Symposium on Biomedical Imaging, 2023

Cross-Modal Contrastive Learning for Robust Representation of the Extracellular Matrix in Static and Dynamic Full-Field OCT Images.
Proceedings of the 20th IEEE International Symposium on Biomedical Imaging, 2023

Probing Intracellular Elasticity with Minimal-Hessian Registration.
Proceedings of the 20th IEEE International Symposium on Biomedical Imaging, 2023

Sparse Non-Negative Matrix Factorization for Preclinical Bioluminescent Imaging.
Proceedings of the 20th IEEE International Symposium on Biomedical Imaging, 2023

Ensemble Multiple Instance Learning for Bladder Cancer Diagnosis.
Proceedings of the 20th IEEE International Symposium on Biomedical Imaging, 2023

2022
Spatial Analysis For Histopathology: A Statistical Approach.
Proceedings of the 19th IEEE International Symposium on Biomedical Imaging, 2022

Statistical Coupling Between time Point-Processes.
Proceedings of the 19th IEEE International Symposium on Biomedical Imaging, 2022

Characterizing Cell Populations Using Statistical Shape Modes.
Proceedings of the 19th IEEE International Symposium on Biomedical Imaging, 2022

Cell Instance Segmentation Using Z-Stacks in Digital Cytology.
Proceedings of the 19th IEEE International Symposium on Biomedical Imaging, 2022

Characterizing Cell Shape Distributions Using k-Mode Kernel Mixtures.
Proceedings of the 26th International Conference on Pattern Recognition, 2022

The Lifecycle of a Neural Network in the Wild: A Multiple Instance Learning Study on Cancer Detection from Breast Biopsies Imaged with Novel Technique.
Proceedings of the 2022 IEEE International Conference on Image Processing, 2022

PDE-Constrained Optimization for Nuclear Mechanics.
Proceedings of the 2022 IEEE International Conference on Image Processing, 2022

Smart Learning of Click and Refine for Nuclei Segmentation on Histology Images.
Proceedings of the 2022 IEEE International Conference on Image Processing, 2022

2021
Evaluating the Stability of Spatial Keypoints via Cluster Core Correspondence Index.
IEEE Trans. Image Process., 2021

Bioimage Analysis and Cell Motility.
Patterns, 2021

Nu3D: 3D Nuclei Segmentation from Light-Sheet Microscopy Images of the Embryonic Heart.
Proceedings of the 18th IEEE International Symposium on Biomedical Imaging, 2021

A Min-Max Based Hyperparameter Estimation For Domain-Adapted Segmentation Of Amoeboid Cells.
Proceedings of the 18th IEEE International Symposium on Biomedical Imaging, 2021

Blind Source Separation In Dynamic Cell Imaging Using Non-Negative Matrix Factorization Applied To Breast Cancer Biopsies.
Proceedings of the 18th IEEE International Symposium on Biomedical Imaging, 2021

Leveraging Global Diagnosis For Tumor Localization In Dynamic Cell Imaging Of Breast Cancer Tissue Towards Fast Biopsying.
Proceedings of the 18th IEEE International Symposium on Biomedical Imaging, 2021

A Robust and Versatile Framework to Compare Spike Detection Methods in Calcium Imaging of Neuronal Activity.
Proceedings of the 18th IEEE International Symposium on Biomedical Imaging, 2021

Morphological Reconstruction of Detached Dendritic Spines via Geodesic Path Prediction.
Proceedings of the 18th IEEE International Symposium on Biomedical Imaging, 2021

2020
Generalizing the Statistical Analysis of Objects' Spatial Coupling in Bioimaging.
IEEE Signal Process. Lett., 2020

Learning to segment clustered amoeboid cells from brightfield microscopy via multi-task learning with adaptive weight selection.
Proceedings of the 25th International Conference on Pattern Recognition, 2020

Extended Depth of Field Preserving Color Fidelity For Automated Digital Cytology.
Proceedings of the 25th International Conference on Pattern Recognition, 2020

Modeling Shape Dynamics During Cell Motility in Microscopy Videos.
Proceedings of the IEEE International Conference on Image Processing, 2020

2019
Tracking and line integration of diffuse cellular subdomains by mesh advection.
Proceedings of the 41st Annual International Conference of the IEEE Engineering in Medicine and Biology Society, 2019

Icytomine: A User-Friendly Tool for Integrating Workflows on Whole Slide Images.
Proceedings of the Digital Pathology - 15th European Congress, 2019

Vector-Based Morphological Operations on Polygons Using Straight Skeletons for Digital Pathology.
Proceedings of the Discrete Geometry for Computer Imagery, 2019

2018
Denoising of Microscopy Images: A Review of the State-of-the-Art, and a New Sparsity-Based Method.
IEEE Trans. Image Process., 2018

Morphological operations on polygons using straight skeletons for digital pathology.
Proceedings of the 15th IEEE International Symposium on Biomedical Imaging, 2018

Basal cell carcinoma detection in full field OCT images using convolutional neural networks.
Proceedings of the 15th IEEE International Symposium on Biomedical Imaging, 2018

Unsupervised analysis of mouse social behaviour reveals how hyperactivity impacts social aspects in a mouse model of autism.
Proceedings of the 15th IEEE International Symposium on Biomedical Imaging, 2018

2017
Multi-staining registration of large histology images.
Proceedings of the 14th IEEE International Symposium on Biomedical Imaging, 2017

Reducing data acquisition for fast Structured Illumination Microscopy using Compressed Sensing.
Proceedings of the 14th IEEE International Symposium on Biomedical Imaging, 2017

Combining global tracking with statistical classification to analyze endocytosis dynamics using TIRF microscopy.
Proceedings of the 14th IEEE International Symposium on Biomedical Imaging, 2017

Quad-edge active contours for biomedical image segmentation.
Proceedings of the 14th IEEE International Symposium on Biomedical Imaging, 2017

Unbiased analysis of mouse social behaviour using unsupervised machine learning.
Proceedings of the 14th IEEE International Symposium on Biomedical Imaging, 2017

2016
A Guided Tour of Selected Image Processing and Analysis Methods for Fluorescence and Electron Microscopy.
IEEE J. Sel. Top. Signal Process., 2016

Introduction to the Issue on Advanced Signal Processing in Microscopy and Cell Imaging.
IEEE J. Sel. Top. Signal Process., 2016

Biophysical measurements in 2D and 3D live cell imaging using fluid dynamics and optical flow.
Proceedings of the 13th IEEE International Symposium on Biomedical Imaging, 2016

Sparsity-based simplification of spectral-domain optical coherence tomography images of cardiac samples.
Proceedings of the 13th IEEE International Symposium on Biomedical Imaging, 2016

An approach for detection of glomeruli in multisite digital pathology.
Proceedings of the 13th IEEE International Symposium on Biomedical Imaging, 2016

2015
Signal Processing Challenges in Quantitative 3-D Cell Morphology: More than meets the eye.
IEEE Signal Process. Mag., 2015

Image denoising by multiple compressed sensing reconstructions.
Proceedings of the 12th IEEE International Symposium on Biomedical Imaging, 2015

Using steerable wavelets and minimal paths to reconstruct automatically filaments in fluorescence imaging.
Proceedings of the 2015 IEEE International Conference on Image Processing, 2015

2014
An Unbiased Risk Estimator for Image Denoising in the Presence of Mixed Poisson-Gaussian Noise.
IEEE Trans. Image Process., 2014

A statistical analysis of spatial clustering along cell filaments using Ripley's K function.
Proceedings of the IEEE 11th International Symposium on Biomedical Imaging, 2014

3D shape analysis using overcomplete spherical wavelets: Application to BLEB detection in cell biology.
Proceedings of the IEEE 11th International Symposium on Biomedical Imaging, 2014

Fluid dynamics modeling of cell and membrane deformations.
Proceedings of the IEEE 11th International Symposium on Biomedical Imaging, 2014

2013
Multiple Hypothesis Tracking for Cluttered Biological Image Sequences.
IEEE Trans. Pattern Anal. Mach. Intell., 2013

Extracting 3D cell parameters from dense tissue environments: application to the development of the mouse heart.
Bioinform., 2013

Image-based representation and modeling of spatiotemporal cell dynamics.
Proceedings of the 10th IEEE International Symposium on Biomedical Imaging: From Nano to Macro, 2013

Phase retrieval with sparsity priors and application to microscopy video reconstruction.
Proceedings of the 10th IEEE International Symposium on Biomedical Imaging: From Nano to Macro, 2013

A statistical analysis of spatial colocalization using Ripley's K function.
Proceedings of the 10th IEEE International Symposium on Biomedical Imaging: From Nano to Macro, 2013

Automatic detection of 3D cell protrusions using spherical wavelets.
Proceedings of the IEEE International Conference on Image Processing, 2013

Icy: A user-friendly environment for algorithm development and deployment.
Proceedings of the 21st European Signal Processing Conference, 2013

2012
Bayesian Estimation for Optimized Structured Illumination Microscopy.
IEEE Trans. Image Process., 2012

Characterization of cell shape and deformation in 3D using Spherical Harmonics.
Proceedings of the 9th IEEE International Symposium on Biomedical Imaging: From Nano to Macro, 2012

Video reconstruction using compressed sensing measurements and 3d total variation regularization for bio-imaging applications.
Proceedings of the 19th IEEE International Conference on Image Processing, 2012

Fluid optical flow for forces and pressure field estimation in cellular biology.
Proceedings of the 19th IEEE International Conference on Image Processing, 2012

2011
3-D Active Meshes: Fast Discrete Deformable Models for Cell Tracking in 3-D Time-Lapse Microscopy.
IEEE Trans. Image Process., 2011

Trends in Bioimaging and Signal Processing [In the Spotlight].
IEEE Signal Process. Mag., 2011

Special issue on whole slide microscopic image processing.
Comput. Medical Imaging Graph., 2011

A fast and automated framework for extraction of nuclei from cluttered 3D images in fluorescence microscopy.
Proceedings of the 8th IEEE International Symposium on Biomedical Imaging: From Nano to Macro, 2011

Wavefront sensing for aberration modeling in fluorescence macroscopy.
Proceedings of the 8th IEEE International Symposium on Biomedical Imaging: From Nano to Macro, 2011

Comparison of reconstruction algorithms in compressed sensing applied to biological imaging.
Proceedings of the 8th IEEE International Symposium on Biomedical Imaging: From Nano to Macro, 2011

Statistical color texture descriptors for histological images analysis.
Proceedings of the 8th IEEE International Symposium on Biomedical Imaging: From Nano to Macro, 2011

ICY: A new open-source community image processing software.
Proceedings of the 8th IEEE International Symposium on Biomedical Imaging: From Nano to Macro, 2011

Image filtering using anisotropic structure tensor for cell membrane enhancement in 3D microscopy.
Proceedings of the 18th IEEE International Conference on Image Processing, 2011

Numerical evaluation of sampling bounds for near-optimal reconstruction in compressed sensing.
Proceedings of the 18th IEEE International Conference on Image Processing, 2011

Spherical Harmonics based extraction and annotation of cell shape in 3D time-lapse microscopy sequences.
Proceedings of the 33rd Annual International Conference of the IEEE Engineering in Medicine and Biology Society, 2011

2010
Combining Local Filtering and Multiscale Analysis for Edge, Ridge, and Curvilinear Objects Detection.
IEEE Trans. Image Process., 2010

Compressed Sensing with off-axis frequency-shifting holography
CoRR, 2010

Compressed sensing for digital holographic microscopy.
Proceedings of the 2010 IEEE International Symposium on Biomedical Imaging: From Nano to Macro, 2010

Improving histology images segmentation through spatial constraints and supervision.
Proceedings of the International Conference on Image Processing, 2010

Curvelet analysis of kymograph for tracking bi-directional particles in fluorescence microscopy images.
Proceedings of the International Conference on Image Processing, 2010

Tracking multiple articulated objects using physics engines: Improvement using multi scale decomposition and quadtrees.
Proceedings of the International Conference on Image Processing, 2010

2009
A Compressed Sensing Approach for Biological Microscopic Image Processing.
Proceedings of the 2009 IEEE International Symposium on Biomedical Imaging: From Nano to Macro, Boston, MA, USA, June 28, 2009

Multiple Hypothesis Tracking in Microscopy Images.
Proceedings of the 2009 IEEE International Symposium on Biomedical Imaging: From Nano to Macro, Boston, MA, USA, June 28, 2009

Using Physics Engines to Track Objects in Images.
Proceedings of the 2009 IEEE International Symposium on Biomedical Imaging: From Nano to Macro, Boston, MA, USA, June 28, 2009

Compressed Sensing in microscopy with random projections in the Fourier domain.
Proceedings of the International Conference on Image Processing, 2009

Multiple hypothesis tracking in cluttered condition.
Proceedings of the International Conference on Image Processing, 2009

Particle tracking in fluorescent microscopy images improved by morphological source separation.
Proceedings of the International Conference on Image Processing, 2009

Tracking articulated objects with physics engines.
Proceedings of the International Conference on Image Processing, 2009

2008
Statistical colocalization in biological imaging with false discovery control.
Proceedings of the 2008 IEEE International Symposium on Biomedical Imaging: From Nano to Macro, 2008

Blind deconvolution for diffraction-limited fluorescence microscopy.
Proceedings of the 2008 IEEE International Symposium on Biomedical Imaging: From Nano to Macro, 2008

Improving single particle localization with an empirically calibrated Gaussian kernel.
Proceedings of the 2008 IEEE International Symposium on Biomedical Imaging: From Nano to Macro, 2008

A multi-threaded program architecture for an asynchronous and highly responsive GUI for automatic neuronal survival quantification.
Proceedings of the 2008 IEEE International Symposium on Biomedical Imaging: From Nano to Macro, 2008

Detection of full length microtubules in live microscopy images.
Proceedings of the 2008 IEEE International Symposium on Biomedical Imaging: From Nano to Macro, 2008

Fast and automatic reconstruction of structured illumination microscopy images with multiscale products.
Proceedings of the 19th International Conference on Pattern Recognition (ICPR 2008), 2008

Automated quantification of cell endocytosis using active contours and wavelets.
Proceedings of the 19th International Conference on Pattern Recognition (ICPR 2008), 2008

Morphological source separation for particle tracking in complex biological environments.
Proceedings of the 19th International Conference on Pattern Recognition (ICPR 2008), 2008

Feature-aided particle tracking.
Proceedings of the International Conference on Image Processing, 2008

Session MA2: Advances in bioimaging and analysis.
Proceedings of the 42nd Asilomar Conference on Signals, Systems and Computers, 2008

Tracking live cells in 4D microscopy: From active surfaces to active meshes.
Proceedings of the 42nd Asilomar Conference on Signals, Systems and Computers, 2008

2007
Multiscale Variance-Stabilizing Transform for Mixed-Poisson-Gaussian Processes and its Applications in Bioimaging.
Proceedings of the International Conference on Image Processing, 2007

Feature-Adapted Fast Slant Stack.
Proceedings of the International Conference on Image Processing, 2007

Detection of Curvilinear Objects in Noisy Image using Feature-Adapted Beamlet Transform.
Proceedings of the IEEE International Conference on Acoustics, 2007

2006
Multiple particle tracking in 3-D+t microscopy: method and application to the tracking of endocytosed quantum dots.
IEEE Trans. Image Process., 2006

On the digital trail of mobile cells.
IEEE Signal Process. Mag., 2006

Automated super-resolution detection of fluorescent rods in 2D.
Proceedings of the 2006 IEEE International Symposium on Biomedical Imaging: From Nano to Macro, 2006

Automated image-based screening of cell cultures for cell therapy.
Proceedings of the 2006 IEEE International Symposium on Biomedical Imaging: From Nano to Macro, 2006

Biophysical Active Contours for Cell Tracking I: Tension and Bending.
Proceedings of the International Conference on Image Processing, 2006

An Overview of Image Analysis in Multidimensional Biological Microscopy.
Proceedings of the 2006 IEEE International Conference on Acoustics Speech and Signal Processing, 2006

2005
Segmenting and Tracking Fluorescent Cells in Dynamic 3-D Microscopy With Coupled Active Surfaces.
IEEE Trans. Image Process., 2005

Coupled Parametric Active Contours.
IEEE Trans. Pattern Anal. Mach. Intell., 2005

A Quantitative Criterion to Evaluate Color Segmentations Application to Cytological Images.
Proceedings of the Advanced Concepts for Intelligent Vision Systems, 2005

2004
Tracking Fluorescent Cells With Coupled Geometric Active Contours.
Proceedings of the 2004 IEEE International Symposium on Biomedical Imaging: From Nano to Macro, 2004

Interacting Multiple Model Based Method to Track Moving Fluorescent Biological Spots.
Proceedings of the 2004 IEEE International Symposium on Biomedical Imaging: From Nano to Macro, 2004

A Deconvolution Method for Confocal Microscopy with Total Variation Regularization.
Proceedings of the 2004 IEEE International Symposium on Biomedical Imaging: From Nano to Macro, 2004

Automatic Color Space Selection for Biological Image Segmentation.
Proceedings of the 17th International Conference on Pattern Recognition, 2004

Split and Merge Data Association Filter for Dense Multi-target Tracking.
Proceedings of the 17th International Conference on Pattern Recognition, 2004

Adaptive gating in gaussian bayesian multi-target tracking.
Proceedings of the 2004 International Conference on Image Processing, 2004

A Quantification Tool to Analyse Stained Cell Cultures.
Proceedings of the Image Analysis and Recognition: International Conference, 2004

2003
Tracking of multiple fluorescent biological objects in three dimensional video microscopy.
Proceedings of the 2003 International Conference on Image Processing, 2003

2002
Segmentation and Tracking of Migrating Cells in Videomicroscopy with Parametric Active Contours: A Tool for Cell-Based Drug Testing.
IEEE Trans. Medical Imaging, 2002

Extraction of spots in biological images using multiscale products.
Pattern Recognit., 2002

Quantitative analysis of cellular shape and motility with improved active contours.
Proceedings of the 2002 IEEE International Symposium on Biomedical Imaging, 2002

Improving Active Contours for Segmentation and Tracking of Motile Cells in Videomicroscopy.
Proceedings of the 16th International Conference on Pattern Recognition, 2002

Color Image Segmentation Based on Markov Random Field Clustering for Histological Image Analysis.
Proceedings of the 16th International Conference on Pattern Recognition, 2002

2001
Three dimensional spot detection by multiscale analysis.
Proceedings of the 2001 International Conference on Image Processing, 2001

2000
Active Contours for the Movement and Motility Analysis of Biological Objects.
Proceedings of the 2000 International Conference on Image Processing, 2000

1997
A Wavelet-Based Multiresolution Method to Automatically Register Images.
J. Math. Imaging Vis., 1997

Adaptive detection for tracking moving biological objects in video microscopy sequences.
Proceedings of the Proceedings 1997 International Conference on Image Processing, 1997

1996
Automatic detection of spots in biological images by a wavelet-based selective filtering technique.
Proceedings of the Proceedings 1996 International Conference on Image Processing, 1996

1994
Automatic Threshold Selection Using the Wavelet Transform.
CVGIP Graph. Model. Image Process., 1994

1993
Image segmentation by wavelet-based automatic threshold selection.
Proceedings of the Visual Communications and Image Processing '93, 1993


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