MORPHEME Research team
Morphologie et Images
- Leader : Xavier Descombes
- Type : Project team
- Research center(s) : Sophia
- Field : Digital Health, Biology and Earth
- Theme : Computational Biology
- Partner(s) : CNRS,Université Nice - Sophia Antipolis
- Collaborator(s) : Laboratoire informatique, signaux systèmes de Sophia Antipolis (I3S) (UMR7271),Institut de Biologie de Valrose (UMR7277)
The scientific objectives of MORPHEME are to characterize and model the development and the morphological properties of biological structures from the cell to the supra-cellular scale. Being at the interface between computational science and biology, we plan to understand the morphological changes that occur during development combining in vivo imaging, image processing and computational modelling. The morphology and topology of mesoscopic structures, indeed, do have a key influence on the functional behaviour of organs. Our goal is to characterize different populations or development conditions based on the shape of cellular and supra-cellular structures, including micro-vascular networks and dendrite/axon networks. Using 2D, 2D+t, 3D or 3D+t images (acquired with confocal microscopy, video-microscopy, 2-photon microscopy or micro-tomography), we plan to extract quantitative parameters to characterize morphometry over time and in different samples. We then statistically analyse shapes and complex structures to identify relevant markers and define classification tools. Finally, we propose models explaining the temporal evolution of the observed samples. With this, we hope to better understand the development of normal tissues, but also characterize at the supra-cellular level different pathologies such as the Fragile X Syndrome, Alzheimer or diabetes.
- Image acquisition: this includes i) from the biological question, definition of studied populations (experimental conditions) and preparation of samples. ii) optimization of the acquisition protocols (staining, imaging,...) and definition of relevant quantitative characteristics. iii) reconstruction/restoration of native data to improve the image readability and interpretation.
- Feature extraction: this consists in detecting and delineating the biological structures of interest from images. This includes the use of previously defined models for improving the detection. Two main challenges are the variability of biological structures and the huge size of data sets.
- Classification/Interpretation: considering a database of images containing different populations, we can infer the parameters associated with a given model on each dataset from which the biological structure under study has been extracted. We define classification schemes for characterizing the different population based either on the model parameters or on some specific metric between the extracted structures. This characterization provides biological information defining the different classes.
- Modelling: Two aspects are considered. This first consists in modelling biological phenomena such as axon growth or network topology in different contexts. One main advantage of our team is the possibility to use the image information for calibrating and/or validating the models. Calibration induces parameter inference as a main challenge. The second aspect consists in using prior model for extracting relevant information from images.
International and industrial relations
- Main French partners :
- CerCo, Toulouse
- IMFT, Toulouse
- JA DIeudonné Lab.
- Pasteur Institute,Paris
- Marne la vallée University
- Main international partners :
- Dobrushin Lab., IITP, Moscow
- Weizmann Institute, Israel
Research teams of the same theme :
- ABS - Algorithms, Biology, Structure
- AMIBIO - Algorithms and Models for Integrative BIOlogy
- BEAGLE - Artificial Evolution and Computational Biology
- BIGS - Biology, genetics and statistics
- BONSAI - Bioinformatics and Sequence Analysis
- CAPSID - Computational Algorithms for Protein Structures and Interactions
- DYLISS - Dynamics, Logics and Inference for biological Systems and Sequences
- ERABLE - European Research team in Algorithms and Biology, formaL and Experimental
- GENSCALE - Scalable, Optimized and Parallel Algorithms for Genomics
- IBIS - Modeling, simulation, measurement, and control of bacterial regulatory networks
- LIFEWARE - Computational systems biology and optimization
- PLEIADE - from patterns to models in computational biodiversity and biotechnology
- SERPICO - Space-timE RePresentation, Imaging and cellular dynamics of molecular COmplexes
- TAPDANCE - Theory and Practice of Nanoscale Computing Engines
- VIRTUAL PLANTS - Modeling plant morphogenesis at different scales, from genes to phenotype