Software

Overview

To better illustrate the differences in cell mobility between different strains, we have developed a software AddTraj2Img.py to visualize the capability of cell motility by displaying cell trajectories directly on images.

To use this software, the prerequisite input files include time-lapse images and data files that contain information of tracked cells.

The output of the software are the modified images that contain marks at the center positions of tracked bacterial cells for a period from the first image (i.e. the earliest one among the whole images) to the current examined image.

Algorithm flowchart

Installation

To use this software, Python need to be installed. It is also recommended to install Visual Studio Code, which will be easier for editing and debugging codes.

Usage

After the software is downloaded, it can be directly opened by Visual Studio Code, and be modified by changing the code lines for input information including image directories, image name and data file as well as setting the directory for saving results. The data file needs to contain the center positions of tracked cells, the frame number that cells are observed and id number of each tracked cell (see example files). In our case, the data file is an excel file, so a function of reading excel file is used. If other format of data file is used, the corresponding reading functions need to be changed as well.

After setting up the input information, run the program to get results. The results are modified time-lapse images that contain cell trajectories. Figure 1 shows the last image (left) of a time series recorded data and the result (right) after it was being modified by the program. These modified images can then be transformed into a video using ImageJ or similar software.

Figure 1. An example image of a time series recorded data (left) and the result after running the program (right)

Example

We have uploaded an example folder in our team's software repository. Please see details at https://gitlab.igem.org/2024/software-tools/thisdl-united/.