PUBLICATION

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

Authors
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, J.Y., Calvat, P., Vernier, P., Frain, M., Lutfalla, G., Kergosien, Y., Suret, P., Remešíková, M., Doursat, R., Sarti, A., Mikula, K., Peyriéras, N., Bourgine, P.
ID
ZDB-PUB-160226-4
Date
2016
Source
Nature communications   7: 8674 (Journal)
Registered Authors
Colin, Ingrid, Duloquin, Louise, Frain, Monique, Lutfalla, Georges, Peyriéras, Nadine, Recher, Gaëlle, Rizzi, Barbara, Savy, Thierry, Vernier, Philippe
Keywords
Biological sciences, Bioinformatics, Developmental biology
MeSH Terms
  • Animals
  • Cell Lineage
  • Cell Proliferation
  • Embryology/methods*
  • Imaging, Three-Dimensional/methods*
  • Microscopy*
  • Sea Urchins
  • Urochordata
  • Workflow*
  • Zebrafish
PubMed
26912388 Full text @ Nat. Commun.
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.
Genes / Markers
Figures
Show all Figures
Expression
Phenotype
Mutations / Transgenics
Human Disease / Model
Sequence Targeting Reagents
Fish
Antibodies
Orthology
Engineered Foreign Genes
Mapping