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Nat Commun. 2016 Feb 25;7:8674. doi: 10.1038/ncomms9674.

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

Author information

1
Complex Systems Institute Paris Ile-de-France (ISC-PIF, UPS3611), CNRS, 75013 Paris, France.
2
Research Center in Applied Epistemology (CREA, UMR7656), CNRS and Ecole Polytechnique, 75005 Paris, France.
3
Multiscale Dynamics in Animal Morphogenesis (MDAM), Neurobiology &Development (N&D, UPR3294), CNRS, 91198 Gif-sur-Yvette, France.
4
BioEmergences Laboratory (USR3695), CNRS, Université Paris-Saclay, 91198 Gif-sur-Yvette, France.
5
Department of Electronics, Information and Systems, University of Bologna, 40126, Italy.
6
Department of Mathematics and Descriptive Geometry, Slovak University of Technology, 81005 Bratislava, Slovakia.
7
Neurobiology &Development (N&D, UPR3294), CNRS, 91198 Gif-sur-Yvette, France.
8
Computing Center of the National Institute for Nuclear Physics and Particle Physics (CC-IN2P3, USR6402), CNRS, 69100 Villeurbanne, France.
9
Dynamics of Membrane Interactions in Normal and Pathological Cells (DIMNP, UMR5235), CNRS and Université Montpellier 2, 34090 Montpellier, France.
10
Medical Informatics and Knowledge Engineering in e-Health (LIMICS, UMR1142), CNRS and Université Paris 13, 93017 Bobigny, France.
11
Laser, Atomic and Molecular Physics Laboratory (UMR8523), CNRS and Université Lille 1-Science and Technology, 59650 Villeneuve-d'Ascq, France.

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.

PMID:
26912388
PMCID:
PMC4773431
DOI:
10.1038/ncomms9674
[Indexed for MEDLINE]
Free PMC Article

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