Nature Communications (Feb 2016)
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,
- Paul Bourgine
Affiliations
- 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
- Department of Mathematics and Descriptive Geometry, Slovak University of Technology
- Dimitri Fabrèges
- Complex Systems Institute Paris Ile-de-France (ISC-PIF, UPS3611), CNRS
- Róbert Špir
- Department of Mathematics and Descriptive Geometry, Slovak University of Technology
- Mark Hammons
- Complex Systems Institute Paris Ile-de-France (ISC-PIF, UPS3611), CNRS
- Róbert Čúnderlík
- Department of Mathematics and Descriptive Geometry, 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
- Department of Mathematics and Descriptive Geometry, 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
- Department of Mathematics and Descriptive Geometry, Slovak University of Technology
- René Doursat
- Complex Systems Institute Paris Ile-de-France (ISC-PIF, UPS3611), CNRS
- Alessandro Sarti
- Department of Electronics, Information and Systems, University of Bologna
- Karol Mikula
- Department of Mathematics and Descriptive Geometry, 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
- DOI
- https://doi.org/10.1038/ncomms9674
- Journal volume & issue
-
Vol. 7,
no. 1
pp. 1 – 10
Abstract
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.
