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

作者：Faure Emmanuel; Savy Thierry; Rizzi Barbara; Melani Camilo; Stasova Olga; Fabreges Dimitri; Spir Robert; Hammons Mark; Cunderlik Robert; Recher Gaelle; Lombardot Benoit; Duloquin Louise; Colin Ingrid; Kollar Jozef; Desnoulez Sophie; Affaticati Pierre; Maury Benoit; Boyreau Adeline; Nief Jean Yves; Calvat Pascal; Vernier Philippe; Frain Monique; Lutfalla Georges; Kergosien Yannick; Suret Pierre; Remesikova Mariana; Doursat Rene^*; Sarti Alessandro; Mikula Karol^*

来源：Nature Communications, 2016, 7(1): 8674.

DOI：10.1038/ncomms9674

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 usingMov-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.

• 出版日期2016-2
• 单位中国医学科学院北京协和医院