Imagerie pour la biologie et la santé (IBS)

Imagerie optique plein champ d'un explant de rétine de souris

Responsable

Emmanuel FORT

Tél. : 01 80 96 30 35

Co-responsable

Ignacio IZEDDIN

Tél. : 01 80 96 30 75

Membres permanents

Michael ATLAN

Tél. : 01 80 96 30 36

Pedro BARAÇAL DE MECÊ

Tél. : 01 80 96 30 51

Claude BOCCARA

Tél. : 01 80 96 30 44

Maïmouna BOCOUM

Tél. : 01 80 96 30 76

Clément CABRIEL

Tél. : 01 80 96 30 59

Bruce DENBY

Emmanuel FORT

Tél. : 01 80 96 30 35

Ros-Kiri ING

Tél. : 01 80 96 30 41

Ignacio IZEDDIN

Tél. : 01 80 96 30 75

Viacheslav MAZLIN

François RAMAZ

Tél. : 01 80 96 30 47

Olivier THOUVENIN

Tél. : 01 80 96 30 51

Actualités

Generation of retinitis pigmentosa patient-derived hiPSC lines (IDVi007-A, IDVi007-B) carrying the RHO c.68C > A variant (p.P23H) and CRISPR/Cas9-corrected isogenic hiPSC lines (IDVi007-A-1, IDVi007-A-2, IDVi007-A-3) Clémençon, M., J. Brogard, M. Rozen, C. Hourton, R. Meléndez García, S. Bigou, S. H. Tsang, O. Thouvenin, K. Grieve, and S. Reichman Stem Cell Research 95, 104042 (2026) Résumé: The p.Pro23His (c.68C > A; P23H) mutation leads to autosomal dominant retinitis pigmentosa (adRP). Here, we reprogrammed adRP patient fibroblasts in human induced pluripotent stem cells (hiPSCs) using Sendai virus. We then generated two mutated hiPSC clones and three isogenic controls using CRISPR/Cas9. All five hiPSC lines express pluripotency genes and are able to differentiate into the three germ layers as well as retinal organoids. Altogether, these hiPSCs constitute unique biological tools to elucidate mechanisms of adRP linked to the RHO-P23H mutation.
Brightness demixing for simultaneous multi-target imaging in 3D single-molecule localization microscopy Le, L., S. K. Sreenivas, E. Fort, and S. Lévêque-Fort Nature Methods (2026) Résumé: Single-molecule localization microscopy has enabled high-resolution imaging, but the simultaneous detection of multiple fluorophores traditionally relies on spectral-based separation, which is inherently constrained by spectral overlap. Here we introduce brightness demixing, a method for fluorophore discrimination that exploits brightness, which directly depends on the fluorophore extinction coefficient and quantum yield. By oversampling blinking events, we precisely quantify photon flux as a proxy for brightness, enabling robust differentiation of fluorophores independent of their spectral properties, without requiring additional spectral separation. Brightness demixing operates within a single detection channel, eliminating the need for additional spectral filters or cameras. We demonstrate this approach with simultaneous two- and three-target imaging in both two- and three-dimensional configurations. By maintaining single-wavelength excitation and minimizing chromatic aberrations, this method notably enhances multiplexing in single-molecule localization microscopy while remaining fully compatible with existing setups. Brightness Demixing thus offers a simple yet powerful approach for expanding multi-target imaging capabilities in super-resolution microscopy.
A novel electrocardiogram-synchronized laser Doppler holography system for cardiac cycle-resolved retinal hemodynamics: development and validation Wood, K., N. Schnorbus, L. Muncharaz, Y. Lahoti, B. A. Siesky, G. Guidoboni, A. V. Vercellin, S. Potash, L. A. Greenberg, M. Atlan, T. Y. P. Chui, R. Rosen, and A. Harris Scientific Reports 16, no. 1 (2026) Résumé: The retinal microvasculature is one of the few sites where the microcirculation can be directly and non-invasively visualized in vivo, offering a unique window into ocular disease and systemic health. In this study we developed and validated a novel imaging platform integrating a custom-built one-lead electrocardiogram (ECG) with laser Doppler holography (LDH), a high-speed imaging technique that captures Doppler-induced phase shifts, for real-time cardiac cycle-resolved assessment of retinal hemodynamics. Twenty-five healthy adults were imaged (five images per eye), with 563 cardiac cycles meeting analysis quality criteria. Internal system latency combined with synchronization offset amounted to less than 5 ms. LDH-derived beat-to-beat intervals closely tracked ECG R-R intervals, with small mean differences (~ 3 ms), demonstrating excellent temporal stability without measurable drift. ECG-retina latencies, defined as time from the ECG R-peak to LDH peak systolic velocity (R-PSV), maximal systolic upslope (R-MaxSlope), and 50% PSV amplitude (R-PSV½), were measured. R-PSV½ mean ± SD was 128 ± 18 ms and showed the highest repeatability (ICC = 0.78, median CV = 4.8%). ECG-retina latencies were moderately associated with age and heart rate, in exploratory analyses. This integrated ECG-LDH platform provides repeatable, synchronized, high-speed, cardiac-resolved retinal hemodynamic measurements and establishes a quantitative framework for studying the eye-heart relationship.
Lightweight Food Localization and Recognition via Multi-Branch Feature Learning and Enhanced Aggregation Zhu, X., Y. Yang, P. Cao, G. Sheng, and B. Denby IEEE Journal of Biomedical and Health Informatics, 1-14 (2026) Résumé: Food image localization and recognition on edge devices is a core task in food computing, enabling convenient dietary monitoring and efficient health management. However, food localization and recognition presents significant challenges due to inherent intra-class variability, inter-class similarity, and non-rigid characteristics. To address these challenges, we propose YOLO-Multi Feature Fusion, a novel multi-feature fusion model for food image localization and recognition. Building upon the YOLOv5 framework, YOLO-Multi Feature Fusion integrates several key components: the Ghost Bottleneck from the lightweight GhostNet, a newly designed Multi-Scale Feature Bottleneck, a Bidirectional Vision Transformer, and an Information Cross-Exchange module. These modules enable the model to comprehensively capture and fuse complex feature information from food images while simultaneously reducing both model parameters and computational load. Extensive evaluations on benchmark datasets (UEC Food100, UEC Food256, and ZSFooD) demonstrate that YOLO-Multi Feature Fusion outperforms existing lightweight detectors. Compared to YOLOv5, YOLO-Multi Feature Fusion achieves mAP improvements of 3.0%, 3.0%, and 0.3% on these datasets, respectively, with parameter reductions of 5.7M, 4.7M, and 4.9M, and computational load reductions of 44.6 GFLOPs, 42.0 GFLOPs, and 42.0 GFLOPs. The source code will be released upon the formal publication of the paper.

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Présentation du thème

Le thème IBS étudie les processus et tissus biologiques de l’échelle nanoscopique à macroscopique. Via l’étude approfondie de l’interaction entre différentes ondes et la matière biologique, de nouvelles méthodes d’imagerie non conventionnelles sont développées. L’imagerie de super-résolution permettant de sonder l’organisation de la matière à l’échelle de la molécule individuelle et de comprendre le transport de ces molécules dans l’environnement de la cellule et en particulier dans le noyau. L’équipe imagerie optique plein champ s’intéresse à l’organisation des tissus biologiques par des techniques de microscopie interférométrique sans marquage, et permettant d’étudier la viabilité des cellules et tissus d’un organisme via le suivi des organelles cellulaires, pour des applications tant de biologie fondamentale que de diagnostic médical in vivo. L’équipe imagerie Doppler holographique de la rétine est spécialisée dans la quantification des flux sanguins dans la rétine de patients humains. Néanmoins, les approches optiques présentées jusqu’à là sont limitées à des faibles profondeurs de pénétration dans le corps humain (en dehors de l’œil transparent). Afin de pouvoir sonder les tissus biologiques plus en profondeur, il devient nécessaire d’utiliser d’autres types d’ondes, en particulier les ondes acoustiques. L’imagerie acousto-optique permet d’obtenir des images de tissus avec un contraste optique à plusieurs millimètres de profondeur en marquant les photons multiplement diffusés grâce aux ondes acoustiques. Finalement, l’utilisation d’ondes acoustiques permet à l’équipe Mouvements de surface de cartographier les déformations vibratoires du thorax sans contact et de manière non invasive.

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