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FastTrack:一个用于跟踪数量不定的可变形物体的开源软件。

FastTrack: An open-source software for tracking varying numbers of deformable objects.

机构信息

Sorbonne Université, CNRS, Institut de Biologie Paris-Seine (IBPS), Laboratoire Jean Perrin (LJP), Paris, France.

出版信息

PLoS Comput Biol. 2021 Feb 11;17(2):e1008697. doi: 10.1371/journal.pcbi.1008697. eCollection 2021 Feb.

Abstract

Analyzing the dynamical properties of mobile objects requires to extract trajectories from recordings, which is often done by tracking movies. We compiled a database of two-dimensional movies for very different biological and physical systems spanning a wide range of length scales and developed a general-purpose, optimized, open-source, cross-platform, easy to install and use, self-updating software called FastTrack. It can handle a changing number of deformable objects in a region of interest, and is particularly suitable for animal and cell tracking in two-dimensions. Furthermore, we introduce the probability of incursions as a new measure of a movie's trackability that doesn't require the knowledge of ground truth trajectories, since it is resilient to small amounts of errors and can be computed on the basis of an ad hoc tracking. We also leveraged the versatility and speed of FastTrack to implement an iterative algorithm determining a set of nearly-optimized tracking parameters-yet further reducing the amount of human intervention-and demonstrate that FastTrack can be used to explore the space of tracking parameters to optimize the number of swaps for a batch of similar movies. A benchmark shows that FastTrack is orders of magnitude faster than state-of-the-art tracking algorithms, with a comparable tracking accuracy. The source code is available under the GNU GPLv3 at https://github.com/FastTrackOrg/FastTrack and pre-compiled binaries for Windows, Mac and Linux are available at http://www.fasttrack.sh.

摘要

分析移动对象的动力学特性需要从记录中提取轨迹,这通常通过跟踪电影来完成。我们编译了一个包含二维电影的数据库,这些电影涵盖了非常不同的生物和物理系统,跨越了广泛的长度尺度,并开发了一种通用的、优化的、开源的、跨平台的、易于安装和使用的、自更新的软件,称为 FastTrack。它可以处理感兴趣区域中不断变化的可变形物体数量,特别适合二维动物和细胞跟踪。此外,我们引入了入侵概率作为电影可跟踪性的新度量,它不需要地面真实轨迹的知识,因为它对少量错误具有弹性,并且可以基于特定的跟踪进行计算。我们还利用 FastTrack 的多功能性和速度实现了一种迭代算法,确定一组几乎优化的跟踪参数-进一步减少了人工干预的数量-并证明 FastTrack 可用于探索跟踪参数空间以优化一批类似电影的交换数量。基准测试表明,FastTrack 比最先进的跟踪算法快几个数量级,具有可比的跟踪精度。源代码可在 https://github.com/FastTrackOrg/FastTrack 下根据 GNU GPLv3 获得,Windows、Mac 和 Linux 的预编译二进制文件可在 http://www.fasttrack.sh 获得。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ef35/7904165/a9e2e419f118/pcbi.1008697.g001.jpg

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