title: A workflow to process 3D+time microscopy images of developing organisms and reconstruct their cell lineage.
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.
authors.affiliation: 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.
authors.forename: Emmanuel
authors.initials: E
authors.lastname: Faure
authors.affiliation: 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.
authors.forename: Thierry
authors.initials: T
authors.lastname: Savy
authors.affiliation: 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.
authors.forename: Barbara
authors.initials: B
authors.lastname: Rizzi
authors.affiliation: 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.
authors.forename: Camilo
authors.initials: C
authors.lastname: Melani
authors.affiliation: Department of Mathematics and Descriptive Geometry, Slovak University of Technology, 81005 Bratislava, Slovakia.
authors.forename: Olga
authors.initials: O
authors.lastname: Stašová
authors.affiliation: 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.
authors.forename: Dimitri
authors.initials: D
authors.lastname: Fabrèges
authors.affiliation: Department of Mathematics and Descriptive Geometry, Slovak University of Technology, 81005 Bratislava, Slovakia.
authors.forename: Róbert
authors.initials: R
authors.lastname: Špir
authors.affiliation: 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.
authors.forename: Mark
authors.initials: M
authors.lastname: Hammons
authors.affiliation: Department of Mathematics and Descriptive Geometry, Slovak University of Technology, 81005 Bratislava, Slovakia.
authors.forename: Róbert
authors.initials: R
authors.lastname: Čúnderlík
authors.affiliation: 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.
authors.forename: Gaëlle
authors.initials: G
authors.lastname: Recher
authors.affiliation: 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.
authors.forename: Benoît
authors.initials: B
authors.lastname: Lombardot
authors.affiliation: 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.
authors.forename: Louise
authors.initials: L
authors.lastname: Duloquin
authors.affiliation: Multiscale Dynamics in Animal Morphogenesis (MDAM), Neurobiology &Development (N&D, UPR3294), CNRS, 91198 Gif-sur-Yvette, France.
authors.forename: Ingrid
authors.initials: I
authors.lastname: Colin
authors.affiliation: Department of Mathematics and Descriptive Geometry, Slovak University of Technology, 81005 Bratislava, Slovakia.
authors.forename: Jozef
authors.initials: J
authors.lastname: Kollár
authors.affiliation: Multiscale Dynamics in Animal Morphogenesis (MDAM), Neurobiology &Development (N&D, UPR3294), CNRS, 91198 Gif-sur-Yvette, France.
authors.forename: Sophie
authors.initials: S
authors.lastname: Desnoulez
authors.affiliation: Neurobiology &Development (N&D, UPR3294), CNRS, 91198 Gif-sur-Yvette, France.
authors.forename: Pierre
authors.initials: P
authors.lastname: Affaticati
authors.affiliation: Multiscale Dynamics in Animal Morphogenesis (MDAM), Neurobiology &Development (N&D, UPR3294), CNRS, 91198 Gif-sur-Yvette, France.
authors.forename: Benoît
authors.initials: B
authors.lastname: Maury
authors.affiliation: 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.
authors.forename: Adeline
authors.initials: A
authors.lastname: Boyreau
authors.affiliation: Computing Center of the National Institute for Nuclear Physics and Particle Physics (CC-IN2P3, USR6402), CNRS, 69100 Villeurbanne, France.
authors.forename: Jean-Yves
authors.initials: JY
authors.lastname: Nief
authors.affiliation: Computing Center of the National Institute for Nuclear Physics and Particle Physics (CC-IN2P3, USR6402), CNRS, 69100 Villeurbanne, France.
authors.forename: Pascal
authors.initials: P
authors.lastname: Calvat
authors.affiliation: Neurobiology &Development (N&D, UPR3294), CNRS, 91198 Gif-sur-Yvette, France.
authors.forename: Philippe
authors.initials: P
authors.lastname: Vernier
authors.affiliation: 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.
authors.forename: Monique
authors.initials: M
authors.lastname: Frain
authors.affiliation: Dynamics of Membrane Interactions in Normal and Pathological Cells (DIMNP, UMR5235), CNRS and Université Montpellier 2, 34090 Montpellier, France.
authors.forename: Georges
authors.initials: G
authors.lastname: Lutfalla
authors.affiliation: 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.
authors.forename: Yannick
authors.initials: Y
authors.lastname: Kergosien
authors.affiliation: Laser, Atomic and Molecular Physics Laboratory (UMR8523), CNRS and Université Lille 1-Science and Technology, 59650 Villeneuve-d'Ascq, France.
authors.forename: Pierre
authors.initials: P
authors.lastname: Suret
authors.affiliation: Department of Mathematics and Descriptive Geometry, Slovak University of Technology, 81005 Bratislava, Slovakia.
authors.forename: Mariana
authors.initials: M
authors.lastname: Remešíková
authors.affiliation: 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.
authors.forename: René
authors.initials: R
authors.lastname: Doursat
authors.affiliation: Department of Electronics, Information and Systems, University of Bologna, 40126, Italy.
authors.forename: Alessandro
authors.initials: A
authors.lastname: Sarti
authors.affiliation: Department of Mathematics and Descriptive Geometry, Slovak University of Technology, 81005 Bratislava, Slovakia.
authors.forename: Karol
authors.initials: K
authors.lastname: Mikula
authors.affiliation: 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.
authors.forename: Nadine
authors.initials: N
authors.lastname: Peyriéras
authors.affiliation: 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.
authors.forename: Paul
authors.initials: P
authors.lastname: Bourgine
mesh_terms: D000818:Animals; D019070:Cell Lineage; D049109:Cell Proliferation; D004626:Embryology / Q000379:methods*; D021621:Imaging, Three-Dimensional / Q000379:methods*; D008853:Microscopy; D012617:Sea Urchins; D014561:Urochordata; D057188:Workflow; D015027:Zebrafish