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.
Citation
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. (2016) A workflow to process 3D+time microscopy images of developing organisms and reconstruct their cell lineage. Nature communications. 7:8674.
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
Expression
Phenotype
Mutations / Transgenics
Human Disease / Model
Sequence Targeting Reagents
Fish
Orthology
Engineered Foreign Genes
Mapping