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Faure E, Savy T, Rizzi B, Melani C, Stašová O, Fabrèges D, Špir R, Hammons M, Čúnderlík R, Recher G, Lombardot B, Duloquin L, Colin I, Kollár J, Desnoulez S, Affaticati P, Maury B, Boyreau A, Nief JY, Calvat P, Vernier P, Frain M, Lutfalla G, Kergosien Y, Suret P, Remešíková M, Doursat R, Sarti A, Mikula K, Peyriéras N, Bourgine P. A workflow to process 3D+time microscopy images of developing organisms and reconstruct their cell lineage. Nat Commun 2016; 7:8674. [PMID: 26912388 PMCID: PMC4773431 DOI: 10.1038/ncomms9674] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Accepted: 09/18/2015] [Indexed: 02/06/2023] Open
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.
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Affiliation(s)
- Emmanuel Faure
- Complex Systems Institute Paris Ile-de-France (ISC-PIF, UPS3611), CNRS, 75013 Paris, France
- Research Center in Applied Epistemology (CREA, UMR7656), CNRS and Ecole Polytechnique, 75005 Paris, France
- Multiscale Dynamics in Animal Morphogenesis (MDAM), Neurobiology & Development (N&D, UPR3294), CNRS, 91198 Gif-sur-Yvette, France
| | - Thierry Savy
- Complex Systems Institute Paris Ile-de-France (ISC-PIF, UPS3611), CNRS, 75013 Paris, France
- Research Center in Applied Epistemology (CREA, UMR7656), CNRS and Ecole Polytechnique, 75005 Paris, France
- Multiscale Dynamics in Animal Morphogenesis (MDAM), Neurobiology & Development (N&D, UPR3294), CNRS, 91198 Gif-sur-Yvette, France
- BioEmergences Laboratory (USR3695), CNRS, Université Paris-Saclay, 91198 Gif-sur-Yvette, France
| | - Barbara Rizzi
- Complex Systems Institute Paris Ile-de-France (ISC-PIF, UPS3611), CNRS, 75013 Paris, France
- Multiscale Dynamics in Animal Morphogenesis (MDAM), Neurobiology & Development (N&D, UPR3294), CNRS, 91198 Gif-sur-Yvette, France
- Department of Electronics, Information and Systems, University of Bologna, 40126, Italy
| | - Camilo Melani
- Complex Systems Institute Paris Ile-de-France (ISC-PIF, UPS3611), CNRS, 75013 Paris, France
- BioEmergences Laboratory (USR3695), CNRS, Université Paris-Saclay, 91198 Gif-sur-Yvette, France
- Department of Electronics, Information and Systems, University of Bologna, 40126, Italy
| | - Olga Stašová
- Department of Mathematics and Descriptive Geometry, Slovak University of Technology, 81005 Bratislava, Slovakia
| | - Dimitri Fabrèges
- Complex Systems Institute Paris Ile-de-France (ISC-PIF, UPS3611), CNRS, 75013 Paris, France
- Multiscale Dynamics in Animal Morphogenesis (MDAM), Neurobiology & Development (N&D, UPR3294), CNRS, 91198 Gif-sur-Yvette, France
- BioEmergences Laboratory (USR3695), CNRS, Université Paris-Saclay, 91198 Gif-sur-Yvette, France
| | - Róbert Špir
- Department of Mathematics and Descriptive Geometry, Slovak University of Technology, 81005 Bratislava, Slovakia
| | - Mark Hammons
- Complex Systems Institute Paris Ile-de-France (ISC-PIF, UPS3611), CNRS, 75013 Paris, France
- Multiscale Dynamics in Animal Morphogenesis (MDAM), Neurobiology & Development (N&D, UPR3294), CNRS, 91198 Gif-sur-Yvette, France
- BioEmergences Laboratory (USR3695), CNRS, Université Paris-Saclay, 91198 Gif-sur-Yvette, France
| | - Róbert Čúnderlík
- Department of Mathematics and Descriptive Geometry, Slovak University of Technology, 81005 Bratislava, Slovakia
| | - Gaëlle Recher
- Complex Systems Institute Paris Ile-de-France (ISC-PIF, UPS3611), CNRS, 75013 Paris, France
- Multiscale Dynamics in Animal Morphogenesis (MDAM), Neurobiology & Development (N&D, UPR3294), CNRS, 91198 Gif-sur-Yvette, France
| | - Benoît Lombardot
- Complex Systems Institute Paris Ile-de-France (ISC-PIF, UPS3611), CNRS, 75013 Paris, France
- Research Center in Applied Epistemology (CREA, UMR7656), CNRS and Ecole Polytechnique, 75005 Paris, France
- Multiscale Dynamics in Animal Morphogenesis (MDAM), Neurobiology & Development (N&D, UPR3294), CNRS, 91198 Gif-sur-Yvette, France
| | - Louise Duloquin
- Complex Systems Institute Paris Ile-de-France (ISC-PIF, UPS3611), CNRS, 75013 Paris, France
- Multiscale Dynamics in Animal Morphogenesis (MDAM), Neurobiology & Development (N&D, UPR3294), CNRS, 91198 Gif-sur-Yvette, France
| | - Ingrid Colin
- Multiscale Dynamics in Animal Morphogenesis (MDAM), Neurobiology & Development (N&D, UPR3294), CNRS, 91198 Gif-sur-Yvette, France
| | - Jozef Kollár
- Department of Mathematics and Descriptive Geometry, Slovak University of Technology, 81005 Bratislava, Slovakia
| | - Sophie Desnoulez
- Multiscale Dynamics in Animal Morphogenesis (MDAM), Neurobiology & Development (N&D, UPR3294), CNRS, 91198 Gif-sur-Yvette, France
| | - Pierre Affaticati
- Neurobiology & Development (N&D, UPR3294), CNRS, 91198 Gif-sur-Yvette, France
| | - Benoît Maury
- Multiscale Dynamics in Animal Morphogenesis (MDAM), Neurobiology & Development (N&D, UPR3294), CNRS, 91198 Gif-sur-Yvette, France
| | - Adeline Boyreau
- Multiscale Dynamics in Animal Morphogenesis (MDAM), Neurobiology & Development (N&D, UPR3294), CNRS, 91198 Gif-sur-Yvette, France
- BioEmergences Laboratory (USR3695), CNRS, Université Paris-Saclay, 91198 Gif-sur-Yvette, France
| | - Jean-Yves Nief
- Computing Center of the National Institute for Nuclear Physics and Particle Physics (CC-IN2P3, USR6402), CNRS, 69100 Villeurbanne, France
| | - Pascal Calvat
- Computing Center of the National Institute for Nuclear Physics and Particle Physics (CC-IN2P3, USR6402), CNRS, 69100 Villeurbanne, France
| | - Philippe Vernier
- Neurobiology & Development (N&D, UPR3294), CNRS, 91198 Gif-sur-Yvette, France
| | - Monique Frain
- Multiscale Dynamics in Animal Morphogenesis (MDAM), Neurobiology & Development (N&D, UPR3294), CNRS, 91198 Gif-sur-Yvette, France
- BioEmergences Laboratory (USR3695), CNRS, Université Paris-Saclay, 91198 Gif-sur-Yvette, France
| | - Georges Lutfalla
- Dynamics of Membrane Interactions in Normal and Pathological Cells (DIMNP, UMR5235), CNRS and Université Montpellier 2, 34090 Montpellier, France
| | - Yannick Kergosien
- Complex Systems Institute Paris Ile-de-France (ISC-PIF, UPS3611), CNRS, 75013 Paris, France
- Multiscale Dynamics in Animal Morphogenesis (MDAM), Neurobiology & Development (N&D, UPR3294), CNRS, 91198 Gif-sur-Yvette, France
- BioEmergences Laboratory (USR3695), CNRS, Université Paris-Saclay, 91198 Gif-sur-Yvette, France
- Medical Informatics and Knowledge Engineering in e-Health (LIMICS, UMR1142), CNRS and Université Paris 13, 93017 Bobigny, France
| | - Pierre Suret
- Laser, Atomic and Molecular Physics Laboratory (UMR8523), CNRS and Université Lille 1-Science and Technology, 59650 Villeneuve-d'Ascq, France
| | - Mariana Remešíková
- Department of Mathematics and Descriptive Geometry, Slovak University of Technology, 81005 Bratislava, Slovakia
| | - René Doursat
- Complex Systems Institute Paris Ile-de-France (ISC-PIF, UPS3611), CNRS, 75013 Paris, France
- Research Center in Applied Epistemology (CREA, UMR7656), CNRS and Ecole Polytechnique, 75005 Paris, France
- Multiscale Dynamics in Animal Morphogenesis (MDAM), Neurobiology & Development (N&D, UPR3294), CNRS, 91198 Gif-sur-Yvette, France
- BioEmergences Laboratory (USR3695), CNRS, Université Paris-Saclay, 91198 Gif-sur-Yvette, France
| | - Alessandro Sarti
- Department of Electronics, Information and Systems, University of Bologna, 40126, Italy
| | - Karol Mikula
- Department of Mathematics and Descriptive Geometry, Slovak University of Technology, 81005 Bratislava, Slovakia
| | - Nadine Peyriéras
- Complex Systems Institute Paris Ile-de-France (ISC-PIF, UPS3611), CNRS, 75013 Paris, France
- Multiscale Dynamics in Animal Morphogenesis (MDAM), Neurobiology & Development (N&D, UPR3294), CNRS, 91198 Gif-sur-Yvette, France
- BioEmergences Laboratory (USR3695), CNRS, Université Paris-Saclay, 91198 Gif-sur-Yvette, France
| | - Paul Bourgine
- Complex Systems Institute Paris Ile-de-France (ISC-PIF, UPS3611), CNRS, 75013 Paris, France
- Research Center in Applied Epistemology (CREA, UMR7656), CNRS and Ecole Polytechnique, 75005 Paris, France
- Multiscale Dynamics in Animal Morphogenesis (MDAM), Neurobiology & Development (N&D, UPR3294), CNRS, 91198 Gif-sur-Yvette, France
- BioEmergences Laboratory (USR3695), CNRS, Université Paris-Saclay, 91198 Gif-sur-Yvette, France
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