Biomedical Image Technologies (BIT)

Research: Microscopy Image Analysis for Biological Understanding

The aim of this activity is to develop image analysis methods that allow processing and measuring data acquired with the most recent state-of-the-art microscopy technologies for biomedical understanding. These technologies provide multidimensional in-vivo observations of organism models such as zebrafish. Thus, image analysis is required to approach new challenges in systems biology at the different genetic, proteomic, cellular, organic and individual levels. Our group develops theory and methods applied mainly to: Embryogenesis reconstruction   Image processing methodologies for filtering, tracking and segmentation based on mathematical morphology that allow reconstructing the cell lineage tree of zebrafish and sea-urchin embryogenesis. In-vivo (3D+T) data are acquired with 2-photon laser scanning microscopy, non-linear harmonic imaging (SHG, THG) and selective plane illumination microscopy (SPIM). Spatio-temporal gene atlas of zebrafish Development of image registration and quantification methods to create a 4D atlas of gene expression domains during early zebrafish embryogenesis using in-situ hybridization techniques. The extraction of both the cellular localizations and the level of expression of different genes at different developmental stages will help the understanding of genetic regulatory networks in their spatio-temporal context. Morphogenesis modeling Definition of high level mathematical descriptors of morphogenesis processes that fit with real observations. The quantitative characterization of the embryonic development provides measurements of similarities and differences among different individuals. Protein registration Development of image registration algorithms to automatically fit protein atomic domain models into medium-resolution 3D electron microscopy reconstructions. Registration of protein model from reference domain 1b7vA0 (blue) to best fitting (red) into target domain 1ls9A0 (mesh)

Zebrafish nuclei tracking (trajectories in red) during gastrulation Animal pole views of the zebrafish 3D Atlas where five genes were registered: gsc (red), chd (purple), spt (green), snail (blue) and atv (yellow) Multi-scale segmentation of neural region in zebrafish embryo at 12 hours post fertilization

Collaborations

• Institut de Neurobiologie Alfred Fessard (CNRS), Gif-sur-Yvette, France.
• Institut des Systèmes Complexes - Paris Île de France ISC-PIF (Paris Île-de-France Complex Systems Institute). Paris (France).
• Laboratoire d'Optique et Biosciences. École Polytechnique. Paris (France).
• Biocomputing Unit. Centro Nacional de Biotecnologia CNB (National Center for Biotechnology). Spain

Some publications

(more can be found on the Publications page)

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• Castro-González, C., Luengo-Oroz, M.A., Duloquin, L., Savy, T., Rizzi, B., Desnoulez, S., Doursat, R., Kergosien, Y.L., Ledesma-Carbayo, M.J., Bourgine, P., Peyriéras, N., Santos, A. "A Digital Framework to Build, Visualize and Analyze a Gene Expression Atlas with Cellular Resolution in Zebrafish Early Embryogenesis". PLoS Comput. Biol., 10(6):e1003670. Jun. 2014.
• Luengo-Oroz, M.A., Pastor-Escuredo, D., Castro-Gonzalez, C., Faure, E., Savy, T., Lombardot, B., Rubio-Guivernau, J.L., Duloquin, L., Ledesma-Carbayo, M.J., Bourgine, P., Peyrieras, N., Santos, A. "3D+t Morphological Processing: Applications to Embryogenesis Image Analysis". IEEE Trans. Image Process., 21(8):3518-3530. 2012.
• Castro-González, C., Ledesma-Carbayo, M.J., Peyriéras, N., Santos, A. "Assembling Models of Embryo Development: Image Analysis and the Construction of Digital Atlases". Birth Defects Res. Part C-Embryo Today-Rev., 96(2):109-120. 2012.
• Luengo-Oroz, M.A., Rubio-Guivernau, J.L., Faure, E., Savy, T., Duloquin, L., Olivier, N., Pastor, D., Ledesma-Carbayo, M.J., Débarre, D., Bourgine, P., Beaurepaire, E., Peyriéras, N., Santos, A. "Methodology for Reconstructing Early Zebrafish Development From In Vivo Multiphoton Microscopy". IEEE Trans. Image Process., 21(4):2335-2340. 2012.
• Rubio-Guivernau, J.L., Gurchenkov, V., Luengo-Oroz, M.A., Duloquin, L., Bourgine, P., Santos, A., Peyrieras, N., Ledesma-Carbayo, M.J. "Wavelet-based image fusion in multi-view three-dimensional microscopy". Bioinformatics, 28(2):238-245. 2012.
• Luengo-Oroz, M.A., Ledesma-Carbayo, M.J.,Peyriéras, N., Santos, A. "Image Analysis for Understanding Embryo Development: A Bridge from Microscopy to Biological Insights". Curr. Opin. Genet. Dev., 21(5):630-637. 2011.
• Olivier, N., Luengo-Oroz, M.A., Duloquin, L., Faure, E., Savy, T., Veilleux, I., Solinas, X., Débarre, D., Bourgine, P., Santos, A., Peyriéras, N., Beaurepaire, E. "Cell Lineage Reconstruction of Early Zebrafish Embryos Using Label-Free Nonlinear Microscopy". Science, 329(5994):967-971. 2010. (Supporting online material)
• Megías, D., Marrero, R., del Peso, B.M., García, M.A., Bravo-Cordero, J.J., García-Grande, A., Santos, A., Montoya, M.C. "Novel lambda FRET spectral confocal microscopy imaging method". Microsc. Res. Tech., 72(1):1-11. 2009.
• Malpica, N., Ortuño, J.E., Santos, A. "A multichannel watershed-based algorithm for supervised texture segmentation". Pattern Recogn. Lett., 24(9-10):1545-1554. 2003.
• Santos, A., Young, I.T.. "Model-Based Resolution: Applying the Theory in Quantitative Microscopy" Appl. Optics, 39(17):2948-2958. 2000.
• Ortiz, C., Santos, A., Vallcorba, I., García-Sagredo, J.M., del Pozo, F. "Automation of FISH spot counting in interphase nuclei: Statistical Validation and Data correction". Cytometry, 31(2):93-99. 1998.
• Santos, A., Ortiz, C., Vaquero, J.J., Peña, J.M., Malpica, N., del Pozo, F. "Evaluation of Autofocus Functions in Molecular Cytogenetic Analysis". J. Microsc, 188(3):264-272. 1997.
• Malpica, N., Ortiz, C., Vaquero, J.J., Santos, A., Vallcorba, I., García-Sagredo, J.M., del Pozo, F. "Applying Watershed Algorithms to the Segmentation of Clustered Nuclei". Cytometry, 28(4):289-297. 1997.