10 results on '"Barbara Rizzi"'
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2. A digital framework to build, visualize and analyze a gene expression atlas with cellular resolution in zebrafish early embryogenesis.
- Author
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Carlos Castro-González, Miguel A Luengo-Oroz, Louise Duloquin, Thierry Savy, Barbara Rizzi, Sophie Desnoulez, René Doursat, Yannick L Kergosien, María J Ledesma-Carbayo, Paul Bourgine, Nadine Peyriéras, and Andrés Santos
- Subjects
Biology (General) ,QH301-705.5 - Abstract
A gene expression atlas is an essential resource to quantify and understand the multiscale processes of embryogenesis in time and space. The automated reconstruction of a prototypic 4D atlas for vertebrate early embryos, using multicolor fluorescence in situ hybridization with nuclear counterstain, requires dedicated computational strategies. To this goal, we designed an original methodological framework implemented in a software tool called Match-IT. With only minimal human supervision, our system is able to gather gene expression patterns observed in different analyzed embryos with phenotypic variability and map them onto a series of common 3D templates over time, creating a 4D atlas. This framework was used to construct an atlas composed of 6 gene expression templates from a cohort of zebrafish early embryos spanning 6 developmental stages from 4 to 6.3 hpf (hours post fertilization). They included 53 specimens, 181,415 detected cell nuclei and the segmentation of 98 gene expression patterns observed in 3D for 9 different genes. In addition, an interactive visualization software, Atlas-IT, was developed to inspect, supervise and analyze the atlas. Match-IT and Atlas-IT, including user manuals, representative datasets and video tutorials, are publicly and freely available online. We also propose computational methods and tools for the quantitative assessment of the gene expression templates at the cellular scale, with the identification, visualization and analysis of coexpression patterns, synexpression groups and their dynamics through developmental stages.
- Published
- 2014
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3. Region-Based PDEs for Cells Counting and Segmentation in 3D+Time Images of Vertebrate Early Embryogenesis
- Author
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Barbara Rizzi and Alessandro Sarti
- Subjects
Medical physics. Medical radiology. Nuclear medicine ,R895-920 ,Medical technology ,R855-855.5 - Abstract
This paper is devoted to the segmentation of cell nuclei from time lapse confocal microscopy images, taken throughout early Zebrafish embryogenesis. The segmentation allows to identify and quantify the number of cells in the animal model. This kind of information is relevant to estimate important biological parameters such as the cell proliferation rate in time and space. Our approach is based on the active contour model without edges. We compare two different formulations of the model equation and evaluate their performances in segmenting nuclei of different shapes and sizes. Qualitative and quantitative comparisons are performed on both synthetic and real data, by means of suitable gold standard. The best approach is then applied on a number of time lapses for the segmentation and counting of cells during the development of a zebrafish embryo between the sphere and the shield stage.
- Published
- 2009
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4. Understanding Factors Associated With Psychomotor Subtypes of Delirium in Older Inpatients With Dementia
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Rispoli, Vincenzo, Malara, Alba, Spadea, Fausto, Di Cello, Serena, Ceravolo, Francesco, Fabiano, Francesco, Chiaradia, Giuseppe, Gabriele, Amedeo, Lenino, Peluso, Andrea, Taristano, Settembrini, Vincenzo, Capomolla, Domenico, Citrino, Antonella, Scriva, Antonietta, Bruno, Irene, Secchi, Roberto, De Martino, Eugenio, Muccinelli, Roberto, Lupi, Gerardo, Paonessa, Patrizio, Fabbri, Andrea, Passuti, Maria Teresa, Castellari, Sofia, Po, Andrea, Gaggioli, Guido, Varesi, Massimo, Moneti, Paolo, Capurso, Sebastiano, Latini, Vincenzo, Ghidotti, Stefano, Riccardelli, Francesco, Macchi, Maurizio, Rigo, Rosaria, Claudio, Pascale, Angelo, Bosio, Flavio, Cerrato, Benedetta, Bardelli, Boffelli, Stefano, Cassinadri, Angela, Franzoni, Simone, Spazzini, Elena, Andretto, Daniela, Tonini, Gabriele, Andreani, Laura, Coralli, Mirco, Balotta, Antonio, Cancelliere, Roberto, Ballardini, Giorgio, Simoncelli, Margherita, Mancini, Annarita, Strazzacapa, Mara, Fabio, Stefano, De Filippi, Francesco, Giudice, 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Anzuini, Alessandra, Caffarra, Paolo, Barocco, Federica, Spallazzi, Marco, Paolo, Ceda Gian, Simonetta, Morganti, Andrea, Artoni, Chioatto, Paolo, Bortolamei, Sandra, Soattin, Lucia, Ruotolo, Giovanni, Beneamino, Borelli, Giuseppe, Barilaro, Bertazzoli, Marco, Rota, Elisabetta, Adobati, Annamaria, Scarpa, Alberto, Granziera, Serena, Zuccher, Paola, Fabbro, Angela Dal, Zara, Daniela, Lo Nigro, Ambra, Franchetti, Lorena, Toniolo, Marika, Marcuzzo, Cinzia, Rollone, Marco, Guerriero, Fabio, Sgarlata, Carmelo, Massè, Alessandro, Zatti, Giovanni, Piatti, Massimiliano, Graci, Jole, Benati, Giuseppe, Boschi, Federica, Biondi, Mario, Fiumi, Nicoletta, Erika, Tamburini, Locatelli, Sergio Mario, Mauri, Sabrina, Beretta, Mauro, Margheritis, Laura, Desideri, Giovanbattista, Liberatore, Ester, Carucci, Anna Cecilia, Bonino, Paolo, Caput, Margherita, Antonietti, Maria Paola, Polistena, Giuseppe, De la Pierre, Franz, Mari, Marcello, Massignani, Paola, Tombesi, Fabio, Selvaggio, Fabio, Verbo, Brunella, 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Laura, Gabriella, Cacchiò, Comi, Giancarlo, Magnani, Giuseppe, Santangelo, Roberto, Mazzeo, Salvatore, Giuseppe, Magnani, Francesca, Caso, Giordano, Cecchetti, Roberto, Sant'Angelo, Barbieri, Cristina, Giroldi, Liviana, Bandini, Fabio, Masina, Marco, Malservisi, Simona, Cicognani, Annalena, Ricca, Laura, Piccininni, Maristella, Tassinari, Tiziana, Brogi, Davide, Sugo, Annalisa, Alessandra, Filippi, Sonia, Manfredi, Valerio, Vanni, Andrea, Usai Carlo, Enrico, Colombo, Vera, Renna Francesca, Assunta, Sauchella, Gianmaria, Zavarise, Mauro, Prete, Pietro, Bisagni, Roberto, Masini, Salvatore, Carrabetta, Barone, Antonella, Razzano, Monica, Giuseppe, Imperoli, Angela, Bini, Francesco, Serra, Valeria, D'Agostino, Federico, Gianolla, Lucia, Pietrangeli, Antonella, Velardi, Elisabetta, Di Cello, Cristina, Rosati, Nadia, Casali, Maria, Sessa, Luciano, Abruzzi, Chiara, Costanzi, Bini, Paolo, Pignata, Michele, Enrico, Buonagurio, Maria, Vollery, Giovanni, Carrieri, Giorgio, Cioni, Andrea, Toschi, Marco, Metra, Piera, Ranieri, Alberto, Zucchelli, Ceccon, Anna, Magrin, Laura, Marin, Sara, Barbara, Sofia, Marco, Masina, Laura, Ghedini, Matteo, Moroni, Marco, Paragona, Caterina, Pallotti Maria, Carla, Rota, Federica, Gottardi, Clara, Tomasoni, Melania, Cappuccio, Giampaolo, Bonini, Stefano, Guerini, Valeria, Guerini, Lucia, Merla, Giovambattista, Desideri, Ester, Liberatore, Cecilia, Carucci Anna, Maurizio, Tovaglieri, Vera, Renna Frandesca, Nadia, Bongiorni, Grillo, Antonio, Arenare, Francesca, Tonino, Mineo, David, Kanah, Giorgio, Vianello Piero, Ubaldo, Balducci, Vincenzo, Sidoti, Stefano, Montanari, Marino, Formilan, Busonera Flavio, Murelli Teodolindo, Paolo, Albanese, Monica, Maselli, Francesco, Bolzetta, Roberto, Fabris, Paolo, Bonino, DuranteMangoni, Emanuele, Testoni, Michela, Fabio, Di Stefano, Loredana, Seccia, Valeria, Sonzini, Fabiano, Maria, Annabella, Di Giorgio, Salvatore, De Cosmo, Greco, Antonio, Grazia, D'Onofrio, Daniele, Sancarlo, Gianluca, Resta, Renzo, Girardello, Sergio, Minervini, Morena, Boni, Vitali, Mariagrazia, Marina, Pizzoni, Paolo, De Colle, Cristina, Scarpa, Alessandra, Frattola, Orlandini, Francesco, La Regina, Micaela, Desirée, Addesi, Mirella, Filippo, Mario, Bo, Paola, Porrino, Padulo, Filomena, Cristina, Margheriti, Dario, Rolano, Giancarla, Moscatelli, Guido, Radaelli, Elena, Montini, Prete, Cosimo, Marileda, Novello, Igor, Bramuzzo, Nicole, Bertin, Elena, Rinaldo, Paolillo, Ciro, Riccardi, Angela, Claudia, Benedetti, Barbara, Rizzi, Francesca, Montagna, Silvia, Vitali, Chiara, Cutaia, Oliver, Baca, Mauro, Colombo, Eleonora, Marelli, Giuseppe, Procino, Rosaria, Tararà, Maria, Cottino, Davide, Dell'Acqua, Stefania, Cislaghi, Marco, Cairati, Massimo, Porta, Luca, Scaglione, Martina, De Feo, Paola, Vertolli, Lia, Salvati, Sandro, Cinotti, Valentina, De Santis, Erminia, Biferi, Paola, Cheli, Romina, Rebizzo, Minisola, Salvatore, Luciano, Colangelo, Pasquale, Abete, Ilaria, Liguori, Francesca, Curcio, Guglielmo, Spassini, Marco, Engheben, Sara, Rotunno, Paola, Arosio, Claudio, Angelini, Francesco, Reggiani, Alessandro, Cappelli, Simona, Marcheselli, Lara, Fratticci, Paola, Ranzani, Simonetta, Cesarini, Antonella, Cerini, Generoso, Uomo, Fernando, Gallucci, Giuliano, Ceschia, Emanuela, Serra, Mariolina, Sola, Alessandro, Delitala, Chiara, Pes, Giulia, Lobianco, Alessandro, Giani, Famularo, Simone, Sandini, Marta, Pinotti, Enrico, Gianotti, Luca, Antonella, Battuello, Giulia, Pintore, Sante, Giardini, Rossi, Andrea, Rubele, Sofia, Sant, Selena, Marco, Vignati, Danila, Clerici, Fabio, Rosa, Bandirali, Maria Pia, Nicoletta, Cattaneo, Laura, Boffi, Paolo, Tosoni, Luciano, Terranova, Leonello, Avalli, Margherita, Scanziani, Stefania, De Notaris, Pierluigi, Del Santo, Laura, Rossi, Fabiana, Tezza, Giovanna, Cervati, Antonino, Andreolli, Felice, Catalano, Giuseppe, Burattin, Danilo, Fogli, Giovanna, Di Bella, Francesco, Landi, Salini, Sara, Angela, Brunetti Maria, Giorgetta, Cappa, Giovanni, Galvagno, Paola, Cena, Gerardo, Bruno, Silvio, Raspo, Letizia, Semeraro, Sabrina, Pedrotti, Davide, Barra, Rosaria, Rizzo Maria, Maria, Dalise Anna, Raffaele, Prestano, Palmieri, Vincenzo Ostilio, Palasciano, Giuseppe, Belfiore, Anna, Portincasa, Piero, Carlo, Sabbà, Vincenzo, Solfrizzi, Alessia, D'introno, Valiani, Vincenzo, Carolina, Bologna, Tiziana, Ciarambino, Paola, Turelli, Ugo, Pazzaglia, Federica, Rodella, Giacomo, Piana, Castellano, Maurizio, Anna, Garelli, Elisa, Casella, Federica, Campana, Antonietta, Coschignano Maria, Luigi, Marinangeli, Fabio, Lorico, Salvatore, Bazzano, Giuseppe, Menculini, Gelosa, Giorgio, Viviana, Ambrogio Teresa, Piras, Valentina, Andrea, Ciricugno, Alessandra, Bollari, Coen, Daniele, Magliola, Renata, Milanesio, Deborah, Muzzulini, Carlo Lorenzo, Paolo, Fogliacco, Marinella, Turla, Sofia, Cotelli Maria, Marta, Bianchi, Siano, Pietro, Capo, Giuseppe, Napoletano, Rosa, Cecilia, Politi, Mancini, Concetta, Del Buono, Corrado, De Bartolomeo, Giuseppe, Addolorata, Martinelli, Carmen, Cefalogli, Roberto, Cozzi, Giovanni, Virtuani Angelo, Moschettini, Gianfilippo, Franco, Mastroianni, Daniela, Roglia, D'Amico, Gabriella, Mirella, Palella, Endrizzi, Cristina, Trotta, Lucia, Ciarambino, Tiziana, Orazio, Zanetti, Emanuela, Terazzi, Marta, Sacchetti, Thomas, Fleetwood, Giacomo, Tondo, Ignazio, Di Fazio, Andrea, Bruni, Giuseppe, Orsitto, Emanuela, Fabbro, Serena, Amici, Elena, D'Imporzano, Anna, Casanova, Serena, Bertolio, Erika, Nervo, Roberto, Silvestri, Elena, Semproni, Manuela, Pintus, Francesca, Aloe, Angelo, Tagliaccica, Zambon, Antonella, and Di Santo, Simona G.
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- 2020
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5. Macrobenthic Assemblages and the Influence of Microhabitat in a High-Mountain Lake (Northwest Italy)
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Alice Gabetti, Alessandra Maganza, Camilla Mossotto, Barbara Rizzioli, Giuseppe Esposito, Marco Bertoli, Elisabetta Pizzul, Elena Bozzetta, Marino Prearo, and Paolo Pastorino
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alpine lakes ,macroinvertebrates ,microhabitat ,substrate composition ,Biology (General) ,QH301-705.5 - Abstract
High-mountain lakes are freshwater ecosystems situated above the tree line which are known for their remote locations and limited accessibility. These ecosystems host simplified biotic communities primarily concentrated in the littoral zone and dominated by benthic macroinvertebrates that serve as bioindicators of environmental pressures. A two-year monitoring investigation was performed in July 2022 and July 2023 at Nero Lake (Cesana Torinese, Northwest Italy). Five sites along the lakeshore were selected for sampling physicochemical water parameters and macrobenthos. All collected data were analysed to compare trends across years and within specific sites. The results revealed that Nero Lake exhibited consistent macrobenthic communities across the two years studied, but significant differences were observed in its microhabitats. This suggests that substrate type and physicochemical water parameters strongly influence community composition. Chironomidae larvae and Mollusca were the dominant species, showing distinct associations with different substrates and environmental factors from one year to another. These findings contribute to our understanding of the intricate relationships between benthic macroinvertebrates and their environments, highlighting the necessity of detailed, small-scale assessments to comprehend ecosystem dynamics and develop effective conservation strategies.
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- 2024
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6. A workflow to process 3D+time microscopy images of developing organisms and reconstruct their cell lineage
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Thierry Savy, Barbara Rizzi, Benoit Maury, Nadine Peyriéras, Ingrid Colin, Pierre Affaticati, Sophie Desnoulez, Emmanuel Faure, Róbert Čunderlík, Yannick L. Kergosien, Adeline Boyreau, Jozef Kollár, René Doursat, Jean Yves Nief, Philippe Vernier, Mariana Remešíková, Pascal Calvat, Camilo Melani, Mark Hammons, Olga Stašová, Alessandro Sarti, Georges Lutfalla, Benoit Lombardot, Dimitri Fabrèges, Louise Duloquin, Karol Mikula, Gaëlle Recher, Paul Bourgine, Róbert Špir, Monique Frain, Pierre Suret, Institut des Systèmes Complexes - Paris Ile-de-France (ISC-PIF), Centre National de la Recherche Scientifique (CNRS)-Institut Curie [Paris]-Sorbonne Université (SU)-École polytechnique (X)-École normale supérieure - Cachan (ENS Cachan)-Université Paris 1 Panthéon-Sorbonne (UP1), Centre de recherche en épistémologie appliquée (CREA), École polytechnique (X)-Centre National de la Recherche Scientifique (CNRS), Neurobiologie et Développement (N&eD), Centre National de la Recherche Scientifique (CNRS), Réseau National des Systèmes Complexes (RNSC), Centre National de la Recherche Scientifique (CNRS)-CPU-CGE-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), BioEmergences, Université Paris-Sud - Paris 11 (UP11)-Centre National de la Recherche Scientifique (CNRS), Department of Mathematics and Descriptive Geometry, Slovak University of Technology, Slovak University of Technology in Bratislava, Department of Mathematics (STUBA), Institut des Neurosciences Paris-Saclay (NeuroPSI), Centre de Calcul de l'IN2P3 (CC-IN2P3), Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS), Dynamique des interactions membranaires normales et pathologiques (DIMNP), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Université Montpellier 2 - Sciences et Techniques (UM2)-Université Montpellier 1 (UM1), Laboratoire d'Informatique Médicale et Ingénierie des Connaissances en e-Santé (LIMICS), Université Paris 13 (UP13)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU), Laboratoire de Physique des Lasers, Atomes et Molécules - UMR 8523 (PhLAM), Université de Lille-Centre National de la Recherche Scientifique (CNRS), Dipartimento di Elettronica, Informatica e Sistemistica (DEIS), Alma Mater Studiorum Università di Bologna [Bologna] (UNIBO), Department of Electronics, Information and Systems, University of Bologna, École normale supérieure - Cachan (ENS Cachan)-Université Paris 1 Panthéon-Sorbonne (UP1)-École polytechnique (X)-Institut Curie [Paris]-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut National de la Santé et de la Recherche Médicale (INSERM)-CGE-CPU-Centre National de la Recherche Scientifique (CNRS), Institut de Neurobiologie Alfred Fessard (INAF), Université Montpellier 1 (UM1)-Université Montpellier 2 - Sciences et Techniques (UM2)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), École normale supérieure - Cachan (ENS Cachan)-Université Panthéon-Sorbonne (UP1)-Université Paris-Sud - Paris 11 (UP11)-École polytechnique (X)-Institut Curie-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Institut des Neurosciences de Paris-Saclay (Neuro-PSI), Centre National de la Recherche Scientifique (CNRS)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3), and Università di Bologna [Bologna] (UNIBO)
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0301 basic medicine ,Embryology ,Lineage (genetic) ,In silico ,Science ,General Physics and Astronomy ,Computational biology ,Biology ,Bioinformatics ,computer.software_genre ,Article ,General Biochemistry, Genetics and Molecular Biology ,Workflow ,03 medical and health sciences ,[SCCO]Cognitive science ,Imaging, Three-Dimensional ,0302 clinical medicine ,Software ,Animals ,Cell Lineage ,Segmentation ,Urochordata ,Interactive visualization ,[SDV.BDD]Life Sciences [q-bio]/Development Biology ,Zebrafish ,Cell Proliferation ,Microscopy ,Multidisciplinary ,[SDV.NEU.PC]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC]/Psychology and behavior ,business.industry ,General Chemistry ,Tree (data structure) ,030104 developmental biology ,Sea Urchins ,Web service ,business ,computer ,030217 neurology & neurosurgery - Abstract
The quantitative and systematic analysis of embryonic cell dynamics from in vivo 3D+time image data sets is a major challenge at the forefront of developmental biology. Despite recent breakthroughs in the microscopy imaging of living systems, producing an accurate cell lineage tree for any developing organism remains a difficult task. We present here the BioEmergences workflow integrating all reconstruction steps from image acquisition and processing to the interactive visualization of reconstructed data. Original mathematical methods and algorithms underlie image filtering, nucleus centre detection, nucleus and membrane segmentation, and cell tracking. They are demonstrated on zebrafish, ascidian and sea urchin embryos with stained nuclei and membranes. Subsequent validation and annotations are carried out using Mov-IT, a custom-made graphical interface. Compared with eight other software tools, our workflow achieved the best lineage score. Delivered in standalone or web service mode, BioEmergences and Mov-IT offer a unique set of tools for in silico experimental embryology., Quantitative analysis of embryonic cell dynamics from large data sets remains a major challenge in the field of developmental biology. Here the authors develop software and a workflow to reconstruct cell lineage trees from 3D time lapse imaging data sets from several developing organisms including zebrafish, tunicates and sea urchins.
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- 2016
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7. Identification of the optic recess region as a morphogenetic entity in the zebrafish forebrain
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Kei Yamamoto, Charlotte Bureau, Pierre Affaticati, Philippe Vernier, Catherine Pasqualini, Nadine Peyriéras, Barbara Rizzi, Michaël Demarque, Institut des Neurosciences Paris-Saclay (NeuroPSI), Université Paris-Sud - Paris 11 (UP11)-Centre National de la Recherche Scientifique (CNRS), Institut de Neurobiologie Alfred Fessard (INAF), Centre National de la Recherche Scientifique (CNRS), and BioEmergences, CNRS UPS3674
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Models, Anatomic ,endocrine system ,Embryo, Nonmammalian ,Time Factors ,animal structures ,medicine.brain ,Neurogenesis ,[SDV.NEU.NB]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC]/Neurobiology ,ELAV-Like Protein 3 ,Article ,Prosencephalon ,biology.animal ,medicine ,Basic Helix-Loop-Helix Transcription Factors ,Animals ,Zebrafish ,In Situ Hybridization, Fluorescence ,Basal forebrain ,Multidisciplinary ,Microscopy, Confocal ,biology ,Models, Genetic ,[SDV.NEU.PC]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC]/Psychology and behavior ,Cerebrum ,Reverse Transcriptase Polymerase Chain Reaction ,fungi ,Vertebrate ,Gene Expression Regulation, Developmental ,[SDV.NEU.SC]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC]/Cognitive Sciences ,Anatomy ,Zebrafish Proteins ,biology.organism_classification ,Preoptic Area ,Preoptic area ,Repressor Proteins ,medicine.anatomical_structure ,nervous system ,Forebrain ,embryonic structures ,Optic recess ,Neuroscience - Abstract
Regionalization is a critical, highly conserved step in the development of the vertebrate brain. Discrepancies exist in how regionalization of the anterior vertebrate forebrain is conceived since the “preoptic area” is proposed to be a part of the telencephalon in tetrapods but not in teleost fish. To gain insight into this complex morphogenesis, formation of the anterior forebrain was analyzed in 3D over time in zebrafish embryos, combining visualization of proliferation and differentiation markers, with that of developmental genes. We found that the region containing the preoptic area behaves as a coherent morphogenetic entity, organized around the optic recess and located between telencephalon and hypothalamus. This optic recess region (ORR) makes clear borders with its neighbor areas and expresses a specific set of genes (dlx2a, sim1a and otpb). We thus propose that the anterior forebrain (secondary prosencephalon) in teleosts contains three morphogenetic entities (telencephalon, ORR and hypothalamus), instead of two (telencephalon and hypothalamus). The ORR in teleosts could correspond to “telencephalic stalk area” and “alar hypothalamus” in tetrapods, resolving current inconsistencies in the comparison of basal forebrain among vertebrates.
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- 2015
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8. Towards 3D in silico modeling of the sea urchin embryonic development
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Barbara Rizzi, Nadine Peyriéras, Institut de Neurobiologie Alfred Fessard (INAF), Centre National de la Recherche Scientifique (CNRS), Neurobiologie et Développement (N&eD), Institut des Systèmes Complexes - Paris Ile-de-France (ISC-PIF), École normale supérieure - Cachan (ENS Cachan)-Université Paris 1 Panthéon-Sorbonne (UP1)-Université Paris-Sud - Paris 11 (UP11)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Institut Curie [Paris]-École polytechnique (X), and École normale supérieure - Cachan (ENS Cachan)-Université Paris 1 Panthéon-Sorbonne (UP1)-Université Paris-Sud - Paris 11 (UP11)-Université Pierre et Marie Curie - Paris 6 (UPMC)-École polytechnique (X)-Institut Curie [Paris]-Centre National de la Recherche Scientifique (CNRS)
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Sea urchin ,Computer science ,In silico ,Population ,ved/biology.organism_classification_rank.species ,Biophysics ,Morphogenesis ,Nanotechnology ,Synthetic biological circuit ,Computational biology ,Review ,Biochemistry ,Cellular dynamics ,Multiscale digital specimens ,education ,Model organism ,Organism ,education.field_of_study ,In silico modeling ,ved/biology ,Cell Biology ,In vivo imaging ,[SDV.NEU]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC] ,Developmental biology ,Function (biology) - Abstract
International audience; Embryogenesis is a dynamic process with an intrinsic variability whose understanding requires the integration of molecular, genetic, and cellular dynamics. Biological circuits function over time at the level of single cells and require a precise analysis of the topology, temporality, and probability of events. Integrative developmental biology is currently looking for the appropriate strategies to capture the intrinsic properties of biological systems. The "-omic" approaches require disruption of the function of the biological circuit; they provide static information, with low temporal resolution and usually with population averaging that masks fast or variable features at the cellular scale and in a single individual. This data should be correlated with cell behavior as cells are the integrators of biological activity. Cellular dynamics are captured by the in vivo microscopy observation of live organisms. This can be used to reconstruct the 3D + time cell lineage tree to serve as the basis for modeling the organism's multiscale dynamics. We discuss here the progress that has been made in this direction, starting with the reconstruction over time of three-dimensional digital embryos from in toto time-lapse imaging. Digital specimens provide the means for a quantitative description of the development of model organisms that can be stored, shared, and compared. They open the way to in silico experimentation and to a more theoretical approach to biological processes. We show, with some unpublished results, how the proposed methodology can be applied to sea urchin species that have been model organisms in the field of classical embryology and modern developmental biology for over a century.
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- 2013
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9. 3D early embryogenesis image filtering by nonlinear partial differential equations
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Olga Stašová, Alessandro Sarti, Barbara Rizzi, Nadine Peyriéras, Zuzana Krivá, Karol Mikula, Department of Mathematics, Slovak University of Technology, Slovak University of Technology in Bratislava, Institut de Neurobiologie Alfred Fessard (INAF), Centre National de la Recherche Scientifique (CNRS), Développement, évolution et plasticité du système nerveux (DEPSN), Department of Electrical Energy and Information Engineering 'Guglielmo Marconi' (DEI), and Alma Mater Studiorum Università di Bologna [Bologna] (UNIBO)
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Discretization ,Anisotropic diffusion ,Embryonic Development ,Health Informatics ,010103 numerical & computational mathematics ,02 engineering and technology ,01 natural sciences ,Sensitivity and Specificity ,Imaging, Three-Dimensional ,Image Interpretation, Computer-Assisted ,0202 electrical engineering, electronic engineering, information engineering ,Animals ,Radiology, Nuclear Medicine and imaging ,0101 mathematics ,Zebrafish ,Mathematics ,Mean curvature flow ,Finite volume method ,Partial differential equation ,Radiological and Ultrasound Technology ,Mathematical analysis ,Reproducibility of Results ,Signal Processing, Computer-Assisted ,Filter (signal processing) ,Image Enhancement ,Computer Graphics and Computer-Aided Design ,Magnetic Resonance Imaging ,Nonlinear system ,Hausdorff distance ,Subtraction Technique ,020201 artificial intelligence & image processing ,[SDV.NEU]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC] ,Computer Vision and Pattern Recognition ,Algorithm ,Algorithms - Abstract
International audience; We present nonlinear diffusion equations, numerical schemes to solve them and their application for filtering 3D images obtained from laser scanning microscopy (LSM) of living zebrafish embryos, with a goal to identify the optimal filtering method and its parameters. In the large scale applications dealing with analysis of 3D+time embryogenesis images, an important objective is a correct detection of the number and position of cell nuclei yielding the spatio-temporal cell lineage tree of embryogenesis. The filtering is the first and necessary step of the image analysis chain and must lead to correct results, removing the noise, sharpening the nuclei edges and correcting the acquisition errors related to spuriously connected subregions. In this paper we study such properties for the regularized Perona-Malik model and for the generalized mean curvature flow equations in the level-set formulation. A comparison with other nonlinear diffusion filters, like tensor anisotropic diffusion and Beltrami flow, is also included. All numerical schemes are based on the same discretization principles, i.e. finite volume method in space and semi-implicit scheme in time, for solving nonlinear partial differential equations. These numerical schemes are unconditionally stable, fast and naturally parallelizable. The filtering results are evaluated and compared first using the Mean Hausdorff distance between a gold standard and different isosurfaces of original and filtered data. Then, the number of isosurface connected components in a region of interest (ROI) detected in original and after the filtering is compared with the corresponding correct number of nuclei in the gold standard. Such analysis proves the robustness and reliability of the edge preserving nonlinear diffusion filtering for this type of data and lead to finding the optimal filtering parameters for the studied models and numerical schemes. Further comparisons consist in ability of splitting the very close objects which are artificially connected due to acquisition error intrinsically linked to physics of LSM. In all studied aspects it turned out that the nonlinear diffusion filter which is called geodesic mean curvature flow (GMCF) has the best performance.
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- 2010
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10. Segmentation of cells from 3-D confocal images of live zebrafish embryo
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Barbara Rizzi, M. Campana, Camilo Melani, Paul Bourgine, Nadine Peyriéras, C. Zanella, Alessandro Sarti, Karol Mikula, Dipartimento di Elettronica, Informatica e Sistemistica (DEIS), Alma Mater Studiorum Università di Bologna [Bologna] (UNIBO), Développement, évolution et plasticité du système nerveux (DEPSN), Centre National de la Recherche Scientifique (CNRS), Institut de Neurobiologie Alfred Fessard (INAF), C.Zanella, B.Rizzi, C.Melani, M.Campana, P.Bourgine, K.Mikula, N.Peyriera, and A.Sarti
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Embryo, Nonmammalian ,02 engineering and technology ,Pattern Recognition, Automated ,law.invention ,law ,0202 electrical engineering, electronic engineering, information engineering ,MESH: Microscopy, Confocal ,MESH: Pattern Recognition, Automated ,Segmentation ,Computer vision ,MESH: Animals ,Zebrafish ,0303 health sciences ,education.field_of_study ,Microscopy, Confocal ,MESH: Reproducibility of Results ,020201 artificial intelligence & image processing ,[SDV.NEU]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC] ,MESH: Image Enhancement ,Algorithms ,Confocal ,Population ,MESH: Algorithms ,Iterative reconstruction ,MESH: Imaging, Three-Dimensional ,Biology ,Sensitivity and Specificity ,Edge detection ,03 medical and health sciences ,Imaging, Three-Dimensional ,Artificial Intelligence ,Confocal microscopy ,Image Interpretation, Computer-Assisted ,Animals ,Humans ,MESH: Artificial Intelligence ,education ,MESH: Zebrafish ,030304 developmental biology ,MESH: Humans ,business.industry ,Reproducibility of Results ,MESH: Embryo, Nonmammalian ,Image segmentation ,Image Enhancement ,biology.organism_classification ,MESH: Sensitivity and Specificity ,Artificial intelligence ,business ,MESH: Image Interpretation, Computer-Assisted - Abstract
In this paper, we use partial-differential-equation-based segmentation to accurately extract the shapes of membranes and nuclei from time lapse confocal microscopy images, taken throughout early Zebrafish embryogenesis. This strategy is a prerequisite for an accurate quantitative analysis of cell shape and morphodynamics during organogenesis and is the basis for an integrated understanding of biological processes. This data will also serve for the measurement of the variability between individuals in a population. The segmentation of cellular structures is achieved by first using an edge-preserving image filtering method for noise reduction and then applying an algorithm for cell shape reconstruction based on the Subjective Surfaces technique.
- Published
- 2007
- Full Text
- View/download PDF
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