A workflow to process 3D+time microscopy images of developing organisms and reconstruct their cell lineage

Emmanuel Faure, Thierry Savy, Barbara Rizzi, Camilo Melani, Olga Stašová, Dimitri Fabrèges, Róbert Špir, Mark Hammons, Róbert Čúnderlík, Gaëlle Recher, Benoît Lombardot, Louise Duloquin, Ingrid Colin, Jozef Kollár, Sophie Desnoulez, Pierre Affaticati, Benoît Maury, Adeline Boyreau, Jean-Yves Nief, Pascal Calvat, Philippe Vernier, Monique Frain, Georges Lutfalla, Yannick Kergosien, Pierre Suret, Mariana Remešíková, René Doursat (), Alessandro Sarti, Karol Mikula (), Nadine Peyriéras () and Paul Bourgine
Additional contact information
Emmanuel Faure: Complex Systems Institute Paris Ile-de-France (ISC-PIF, UPS3611), CNRS
Thierry Savy: Complex Systems Institute Paris Ile-de-France (ISC-PIF, UPS3611), CNRS
Barbara Rizzi: Complex Systems Institute Paris Ile-de-France (ISC-PIF, UPS3611), CNRS
Camilo Melani: Complex Systems Institute Paris Ile-de-France (ISC-PIF, UPS3611), CNRS
Olga Stašová: Slovak University of Technology
Dimitri Fabrèges: Complex Systems Institute Paris Ile-de-France (ISC-PIF, UPS3611), CNRS
Róbert Špir: Slovak University of Technology
Mark Hammons: Complex Systems Institute Paris Ile-de-France (ISC-PIF, UPS3611), CNRS
Róbert Čúnderlík: Slovak University of Technology
Gaëlle Recher: Complex Systems Institute Paris Ile-de-France (ISC-PIF, UPS3611), CNRS
Benoît Lombardot: Complex Systems Institute Paris Ile-de-France (ISC-PIF, UPS3611), CNRS
Louise Duloquin: Complex Systems Institute Paris Ile-de-France (ISC-PIF, UPS3611), CNRS
Ingrid Colin: Multiscale Dynamics in Animal Morphogenesis (MDAM), Neurobiology & Development (N&D, UPR3294), CNRS
Jozef Kollár: Slovak University of Technology
Sophie Desnoulez: Multiscale Dynamics in Animal Morphogenesis (MDAM), Neurobiology & Development (N&D, UPR3294), CNRS
Pierre Affaticati: Neurobiology & Development (N&D, UPR3294), CNRS
Benoît Maury: Multiscale Dynamics in Animal Morphogenesis (MDAM), Neurobiology & Development (N&D, UPR3294), CNRS
Adeline Boyreau: Multiscale Dynamics in Animal Morphogenesis (MDAM), Neurobiology & Development (N&D, UPR3294), CNRS
Jean-Yves Nief: Computing Center of the National Institute for Nuclear Physics and Particle Physics (CC-IN2P3, USR6402), CNRS
Pascal Calvat: Computing Center of the National Institute for Nuclear Physics and Particle Physics (CC-IN2P3, USR6402), CNRS
Philippe Vernier: Neurobiology & Development (N&D, UPR3294), CNRS
Monique Frain: Multiscale Dynamics in Animal Morphogenesis (MDAM), Neurobiology & Development (N&D, UPR3294), CNRS
Georges Lutfalla: Dynamics of Membrane Interactions in Normal and Pathological Cells (DIMNP, UMR5235), CNRS and Université Montpellier 2
Yannick Kergosien: Complex Systems Institute Paris Ile-de-France (ISC-PIF, UPS3611), CNRS
Pierre Suret: Laser, Atomic and Molecular Physics Laboratory (UMR8523), CNRS and Université Lille 1-Science and Technology
Mariana Remešíková: Slovak University of Technology
René Doursat: Complex Systems Institute Paris Ile-de-France (ISC-PIF, UPS3611), CNRS
Alessandro Sarti: Information and Systems, University of Bologna
Karol Mikula: Slovak University of Technology
Nadine Peyriéras: Complex Systems Institute Paris Ile-de-France (ISC-PIF, UPS3611), CNRS
Paul Bourgine: Complex Systems Institute Paris Ile-de-France (ISC-PIF, UPS3611), CNRS

Nature Communications, 2016, vol. 7, issue 1, 1-10

Abstract: 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.

Date: 2016
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DOI: 10.1038/ncomms9674

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