A workflow to process 3D+time microscopy images of developing organisms and reconstruct their cell lineage
Emmanuel Faure1,2,3, Thierry Savy1,2,3,4, Barbara Rizzi1,3,5
1Complex Systems Institute Paris Ile-de-France (ISC-PIF, UPS3611), CNRS, 75013 Paris, France.
Nature Communications
|February 26, 2016
Summary
BioEmergences is a new workflow for analyzing embryonic cell dynamics in 3D+time images. It accurately reconstructs cell lineage trees, outperforming other tools for developmental biology research.
Area of Science:
- Developmental Biology
- Bioimaging
- Computational Biology
Background:
- Analyzing embryonic cell dynamics in 3D+time image data is crucial but challenging.
- Accurate cell lineage tree reconstruction from live imaging remains a significant hurdle in developmental biology.
Purpose of the Study:
- To present the BioEmergences workflow, a comprehensive solution for reconstructing and visualizing embryonic cell dynamics.
- To offer advanced computational tools for in silico experimental embryology.
Main Methods:
- Developed novel mathematical methods and algorithms for image filtering, nucleus detection, segmentation, and cell tracking.
- Integrated image acquisition, processing, and interactive visualization into a unified workflow.
- Utilized Mov-IT, a graphical interface, for validation and annotation.
Main Results:
- The BioEmergences workflow demonstrated superior performance in cell lineage tree reconstruction.
- Achieved the best lineage score when compared to eight other software tools.
- Successfully applied to zebrafish, ascidian, and sea urchin embryos.
Conclusions:
- BioEmergences provides a robust and accurate solution for analyzing embryonic cell dynamics.
- The workflow, available as standalone or web service, enhances in silico experimental embryology.
- Offers a unique set of tools for developmental biologists studying cell lineage and dynamics.
