Install

Clone this repository and install requirements.txt

$ git clone https://github.com/TZW-056/Single-bacterium-tracking.git
$ cd Single-bacterium-tracking
$ pip install -r requirements.txt

Usage

The following is the structure of this repository.

.
│  .gitignore
│  README.md
│  requirements.txt  
│
├─data
│  ├── Test-B02.avi  # 20% brighter than the original video
│  ├── Test-R2.avi   # double size of the original video
│  └── Test.avi      # the original video
│      
├─outputs
│   ├── B00.png    # trajectory figure according to Test_yxt.xlsx
│   ├── B20.png    # trajectory figure according to Test-B02_yxt.xlsx
│   ├── Test-B02_yxt.xlsx # trajectory data obtained by processing the Test-B02.avi 
│   └── Test_yxt.xlsx  # trajectory data obtained by processing the Test.avi
│      
└─src
   ├── Plot.py         # visualization trajectory data
   ├── SBTAnalyzer.py  # extraction of bacterial trajectories
   └── utils.py        # some needed functiones

The input video formats that SBTAnalyzer.py supports are .avi .mp4 and the outputs will be stored in the ./outputs folder with the suffix name of .xlsx. What's more, Plot.py can produce the trajectory figure according to the output of SBTAnalyzer.py

NOTE: Test-B02.avi and Test-R2.avi were obtained by ffmpeg.

License

Apache Licence 2.0