FCUP - Faculdade de Ciências da Universidade do Porto, Rua do Campo Alegre s/n, Porto 4169-007, Portugal; INESC-TEC - Instituto de Engenharia de Sistemas e Computadores, Tecnologia e Ciência, Campus da Faculdade de Engenharia da Universidade do Porto, Rua Dr. Roberto Frias, Porto 4200-465, Portugal.
ISEP - Instituto Superior de Engenharia do Porto, Politécnico do Porto, Rua Dr. Antnio Bernardino de Almeida 431, Porto 4249-015, Portugal; i3S - Instituto de Investigação em Saúde, Universidade do Porto, Rua Alfredo Allen 208, Porto 4200-135, Portugal.
Comput Methods Programs Biomed. 2022 Jan;213:106529. doi: 10.1016/j.cmpb.2021.106529. Epub 2021 Nov 14.
Cell migration is essential for many biological phenomena with direct impact on human health and disease. One conventional approach to study cell migration involves the quantitative analysis of individual cell trajectories recorded by time-lapse video microscopy. Dedicated software tools exist to assist the automated or semi-automated tracking of cells and translate these into coordinate positions along time. However, cell biologists usually bump into the difficulty of plotting and computing these data sets into biologically meaningful figures and metrics.
This report describes MigraR, an intuitive graphical user interface executed from the RStudio (via the R package Shiny), which greatly simplifies the task of translating coordinate positions of moving cells into measurable parameters of cell migration (velocity, straightness, and direction of movement), as well as of plotting cell trajectories and migration metrics. One innovative function of this interface is that it allows users to refine their data sets by setting limits based on time, velocity and straightness.
MigraR was tested on different data to assess its applicability. Intended users of MigraR are cell biologists with no prior knowledge of data analysis, seeking to accelerate the quantification and visualization of cell migration data sets delivered in the format of Excel files by available cell-tracking software.
Through the graphics it provides, MigraR is an useful tool for the analysis of migration parameters and cellular trajectories. Since its source code is open, it can be subject of refinement by expert users to best suit the needs of other researchers. It is available at GitHub and can be easily reproduced.
细胞迁移对于许多生物学现象至关重要，对人类健康和疾病有着直接影响。传统的研究细胞迁移的方法之一是通过延时视频显微镜记录细胞的个体轨迹，进行定量分析。有专门的软件工具可以辅助细胞的自动或半自动追踪，并将这些轨迹转化为随时间变化的坐标位置。然而，细胞生物学家通常会遇到将这些数据点绘制并计算成有生物学意义的图形和指标的困难。
本报告描述了 MigraR，这是一个直观的图形用户界面，可从 RStudio（通过 R 包 Shiny）执行，它极大地简化了将移动细胞的坐标位置转化为可测量的细胞迁移参数（速度、直线度和运动方向）的任务，以及绘制细胞轨迹和迁移指标的任务。该界面的一个创新功能是，它允许用户根据时间、速度和直线度设置限制，来精炼他们的数据。
MigraR 在不同的数据上进行了测试，以评估其适用性。MigraR 的预期用户是没有数据分析先验知识的细胞生物学家，他们希望通过现有的细胞追踪软件，加速以 Excel 文件格式提供的细胞迁移数据集的量化和可视化。
通过它提供的图形，MigraR 是分析迁移参数和细胞轨迹的有用工具。由于它的源代码是开放的，因此可以由专家用户进行改进，以最符合其他研究人员的需求。它可以在 GitHub 上获得，并可以轻松复制。
