ingallslab / Trackrefiner

analyzing CellProfiler output

Trackrefiner

Analyzing CellProfiler output

How can I install the Trackrefiner package?

1. Download the most recent version of the package. For beta versions, check the dev branch.
2. Extract the files and navigate to the folder where you downloaded the package
3. Execute the following command:

pip install -e .

Additionally, you can set it up in a new conda environment using these commands:

conda env create -f environment.yml
pip install -e .

Required dependencies for this package include

• numpy
• scipy
• pandas
• scikit-learn
• matplotlib
• opencv-python
• scikit-image

How do I execute the package?

To execute it, run the runPostProcessing.py file in your terminal. To understand the script's arguments, you can execute the following script:

python runPostProcessing.py -h

Inputs required to run this package

1. The output CSV file from "CP" which contains information about measured features of bacteria, such as length, orientation, etc., as well as tracking information. See an example here.
2. The folder contains files in the npy format, which are the results of segmentation, where the pixels of an object are unified in a specific color. See an example here.
3. CSV file containing neighboring data of bacteria. See an example here.