The BioEmergences workflow spans from the acquisition of microscopy images to the interactive visualization of reconstructed data. Two-photon microscopy datasets obtained from developing embryos (sea urchin, zebrafish, tunicates) are processed to reconstruct cell lineage trees. The processing workflow includes original algorithmic steps for image filtering, nucleus center detection, nucleus and membrane segmentation, and cell tracking. Subsequent validation, correction, annotation, and analysis are carried out using Mov-IT, a custom-made interactive visualization software. The BioEmergences cell-tracking pipeline and Mov-IT functionalities are available both as a standalone software and as a webservice, offering a unique set of tools for in silico experimental embryology.

Snapshots, zebrafish, tailbud stage. A: Raw data section at 100 m from animal pole. B: Display of detected nuclei and cell trajectories. Scale bar 100 m. C: Selected clones (colored cubes) and their trajectories raw data orthoslice in white (Faure et al. Nature Comm. 2015 in press).

We propose a two hours tutorial to:
– register as a BioEmergences user
– access the BioEmergences webservice
– fill a typical datasheet for a time lapse experiment
– upload raw image data acquired from a Leica MLSM (.lif file)
– process the data for nucleus center detection and cell tracking
– visualize the data with Mov-IT, validate it, correct it and download the reconstructed cell lineage tree data


Nadine Peyriéras



Photos by : Derek K. Miller