MitoTrack, a user-friendly semi-automatic software for lineage tracking in living embryos

During development, progenitor cells undergo multiple rounds of cellular divisions during which transcriptional programs must be faithfully propagated. To study mitotic inheritance of these programs, it is essential to be able to track transcriptional activities and their transmission from mother to daughter cells in living embryos. Given the stochastic nature of the phenomena, it is necessary to collect and analyze big amount of data to look at the statistical distribution of the results. For this purpose, we developed MitoTrack, a custom build software, developed in PythonTM with a user-friendly graphical user interface (GUI) which provides graphical tools for manual corrections, visualization and check of the results. In order to study the temporal activation of transcriptions in consecutive cell cycles, MitoTrack tracks nuclei across mitosis keeping lineage information and detecting the appearance of transcriptional sites. As a result, we can extract the activation time of each nucleus and its daughters allowing us to study transcriptional memory across mitosis.

Bioinformatics. 2019 Oct 3. pii: btz717. doi: 10.1093/bioinformatics/btz717. [Epub ahead of print]
MitoTrack, a user-friendly semi-automatic software for lineage tracking in living embryos.
Trullo A, Dufourt J, Lagha M.



Fig. 1. MitoTrack GUI to track transcriptional activation and nuclei lineage. (a) Main window composed of four distinct panels, among which, two are shown here, with raw nuclei channel (upper left) and detected nuclei (upper right). MitoTrack typical tools and edit boxes are shown on the left. (b) ‘Modifier Mitosis Tool’ showing all its commands and parameters. Three typical images of nuclei at a time t, t + 1 and their overlap are shown to illustrate the basis of the algorithm for automatic nuclei tracking during mitosis. (c) Interface of the ‘Modify Segmentation Tool’ with its main commands visible. Exemplary results of manual corrections of nuclei segmentation
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