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

Faure, E and Savy, T and Rizzi, B and Melani, C and Stašová, O and Fabrèges, D and Špir, R and Hammons, M and Čunderlík, R and Recher, G and Lombardot, B and Duloquin, L and Colin, I and Kollár, J and Desnoulez, S and Affaticati, P and Maury, B and Boyreau, A and Nief, JY and Calvat, P and Vernier, P and Frain, M and Lutfalla, G and Kergosien, Y and Suret, P and Remešíková, M and Doursat, R and Sarti, A and Mikula, K and Peyriéras, N and Bourgine, P (2016) A workflow to process 3D+time microscopy images of developing organisms and reconstruct their cell lineage. Nature Communications, 7. ISSN 2041-1723

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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.

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