Functional causality in regulating cell morphogenesis

摘要 近二十年来，Danuser实验室已经开发了一系列用于实时显微镜图像的软件 分析，包括粒子跟踪。在2008年的一篇里程碑式的论文中，该实验室引入了一种通用算法 用于对相互作用和部分不稳定的粒子图像的密集场进行稳健跟踪的平台。软件， 从那时起，名为u-Track的系统一直在定义粒子跟踪的最新技术，粒子跟踪是 从超分辨率和单分子研究到组织研究的活显微镜数据分析 发展和动态平衡。U-Track的算法核心已经被广泛使用 Trackmate/ImageJ和CellProfiler开放科学软件包以及商业软件 像Imaris和Amira这样的平台。尽管如此，u-Track作为独立的专业软件仍然很受欢迎。 粒子跟踪应用程序包因为有许多高级功能，这些采用没有 包括。劳顾会已作出重大努力，维持u-Track作为一个方便使用的套装，并支持 通过与用户群体的协商。在过去的四年里，该实验室扩展了u-Track的功能 对于延时3D图像堆栈的分析，由于 光片显微镜的迅速发展。特别是使用u-track3D，许多实验室将缺乏必要的 用于分析这些海量数据集的计算基础设施，并安装专门的开放源码 部门或机构高性能计算基础设施上的软件可能会很麻烦。 此外，我们实验室维护U-Track平台的负担适当地向前和向后 版本兼容性已变得非常重要。因此，我们提出一项为期一年的计划，以补充 最近资助的Mira Grant R35 GM136428-01用于迁移当前的u-Track和u-track3D软件包 集成到一个名为u-trackAll的集装化管道中，用于平台无关的基于云的和/或本地计算。 具体地说，我们将目标1：开发U-TrackAll将U-Track和U-track3D结合成通用的粒子跟踪 平台；目标2：将u-trackAll开发为容器中介的、平台竞争的工作流；目标3：开发 混合(本地+云)交互数据可视化的策略。这项工作将由一个项目团队执行 由现任Danuser实验室软件工程师和德克萨斯大学西南分校的一名软件工程师组成 生物信息学核心设施，雇佣了一群致力于组装开放的软件开发人员 科学软件工作流程。

Abstract For almost twenty years the Danuser lab has developed a wide range of software for live microscopy image analysis, including particle tracking. In a landmark paper in 2008 the lab introduced a versatile algorithmic platform for the robust tracking of dense fields of interacting and partially unstable particle images. The software, called u-track, has ever since been defining the state-of-art for particle tracking, which is an ubiquitous task in the analysis of live microscopy data, from super-resolution and single molecule studies to studies of tissue development and homeostasis. The algorithmic core of u-track has been adopted by the widely-used TrackMate/ImageJ and CellProfiler open science software packages, as well as by commercial software platforms like Imaris and Amira. Nonetheless, u-track retained its popularity as standalone, specialized software package for particle tracking applications because of numerous advanced features these adoptions did not include. The lab has made a significant effort in maintaining u-track as a user-friendly package and in supporting the user community through consultations. Over the past four years the lab has expanded u-track's functionality for the analysis of time-lapse 3D image stacks, which are becoming more and more ubiquitous thanks to the rapid development of light-sheet microscopy. Especially with u-track3D many labs will lack the necessary computing infrastructure for the analysis of these massive data sets, and installation of a specialized open source software on a departmental or institutional high-performance computing infrastructure can be cumbersome. Moreover, the burden on our lab of maintaining the u-track platform with appropriate backward and forward version compatibility has become significant. Therefore, we propose a one year project supplementing the recently funded MIRA grant R35 GM136428-01 to migrate the current u-track and u-track3D software packages into a containerized pipeline, called u-trackAll, for platform-agnostic cloud-based and/or local computation. Specifically we will, Aim 1: Develop u-trackAll combining u-track and u-track3D into a generic particle tracking platform; Aim 2: Develop u-trackAll as a container-mediated, platform-agonistic workflow; Aim 3: Develop strategies for hybrid (local + cloud) interactive data visualization. The work will be performed by a project team composed of the current Danuser lab software engineer and a software engineer in UT Southwestern's Bioinformatics Core Facility, which employs a group of software developers dedicated to the assembly of open science software workflows.