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BioCell2XML: a novel tool for converting cell lineage data from SIMI BioCell to MaMuT (Fiji)

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Abstract

Computer-assisted 4D manual cell tracking has been a valuable method for understanding spatial-temporal dynamics of embryogenesis (e.g., Stach & Anselmi BMC Biol, 13(113), 1–11 2015; Vellutini et al. BMC Biol, 15(33), 1–28 2017; Wolff et al. eLife, 7, e34410 2018) since the method was introduced in the late 1990s. Since two decades SIMI® BioCell (Schnabel et al. Dev Biol, 184, 234–265 1997), a software which initially was developed for analyzing data coming from the, at that time new technique of 4D microscopy, is in use. Many laboratories around the world use SIMI BioCell for the manual tracing of cells in embryonic development of various species to reconstruct cell genealogies with high precision. However, the software has several disadvantages: limits in handling very large data sets, the virtually no maintenance over the last 10 years (bound to older Windows versions), the difficulty to access the created cell lineage data for analyses outside SIMI BioCell, and the high cost of the program. Recently, bioinformatics, in close collaboration with biologists, developed new lineaging tools that are freely available through the open source image processing platform Fiji. Here we introduce a software tool that allows conversion of SIMI BioCell lineage data to a format that is compatible with the Fiji plugin MaMuT (Wolff et al. eLife, 7, e34410 2018). Hereby we intend to maintain the usability of SIMI BioCell created cell lineage data for the future and, for investigators who wish to do so, facilitate the transition from this software to a more convenient program.

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Acknowledgements

We are grateful to Tim Strickler for helping with color conversion from OLE code, to Thomas Stach for providing example data sets of Psammechinus sp. for this study, and to Bruno Vellutini for assisting with the use of simi2mamut. We also would like to thank Bruno Vellutini for the helpful comments on the manuscript.

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Authors and Affiliations

  1. Institut für Biologie, Vergleichende Zoologie, Humboldt-Universität zu Berlin, Philippstr 13, Haus 2, 10115, Berlin, Germany

    Markus Pennerstorfer, Günther Loose & Carsten Wolff

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  1. Markus Pennerstorfer
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  2. Günther Loose
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  3. Carsten Wolff
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Correspondence to Markus Pennerstorfer, Günther Loose or Carsten Wolff.

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Communicated by Angelika Stollewerk

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Pennerstorfer, M., Loose, G. & Wolff, C. BioCell2XML: a novel tool for converting cell lineage data from SIMI BioCell to MaMuT (Fiji). Dev Genes Evol 229, 137–145 (2019). https://doi.org/10.1007/s00427-019-00633-9

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  • DOI: https://doi.org/10.1007/s00427-019-00633-9

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