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.

中文翻译：

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BioCell2XML：一种用于将细胞谱系数据从SIMI BioCell转换为MaMuT（Fiji）的新颖工具。

计算机辅助的4D手动细胞跟踪已成为了解胚胎发生时空动态的有价值的方法（例如，Stach和Anselmi BMC Biol，13（113），2015年11月11日； Vellutini等人，BMC Biol，15（33） ，2017年1月28日； Wolff等人，eLife，7，e34410 2018），因为该方法是在1990年代后期引入的。自从SIMI®BioCell进入二十年以来（Schnabel等，Dev Biol，184，234–265，1997），最初开发了一种软件来分析来自当时4D显微镜新技术的数据。全球许多实验室都使用SIMI BioCell用于在各种物种的胚胎发育中手动追踪细胞，以高精度重建细胞谱系。但是，该软件有几个缺点：处理非常大的数据集有局限性，过去10年几乎没有维护（绑定到较旧的Windows版本），难以访问创建的细胞谱系数据进行SIMI BioCell之外的分析，以及该程序的成本很高。最近，生物信息学与生物学家密切合作，开发了新的谱系工具，这些工具可以通过开源图像处理平台Fiji免费获得。在这里，我们介绍了一种软件工具，该工具可以将SIMI BioCell谱系数据转换为与斐济兼容的格式MaMuT插件（Wolff等人eLife，7，e34410 2018）。因此，我们打算在将来维持SIMI BioCell创建的细胞谱系数据的可用性，并且对于希望这样做的研究人员，促进从该软件到更方便程序的过渡。