Python project for 1D automated single-cell migration assay. Pipeline which takes in a set of raw microscopy imaging data and creates 1D tracks for each detected cell's nucleus, rear and front position. The cells are first segmented using cellpose and the fluorescently labeled nuclei are tracked using trackpy. The project also provides two different tools for visualising the data. Either in a jupyter notebook or as a website.
conda create -n onedcelltrack python=3.8
Install onedcelltrack
python -m pip install git +https://github.com/miguelatienza/onedcelltrack
Activate the conda environment
conda activate onedcelltrack
Copy the notebook templates/run_full_experiment.ipynb to your working directory of choice.
Activate the environment and run jupyterlab :
conda activate onedcelltrack
jupyter-lab
Fill in the notebook and run it.
Copy the Notebook templates/view_results.ipynb to your working directory and view your results.
The website provides a more user friendly interface to interact with the microscopy data and resulting cell trajectories. It can be run on a single host server where the (typically large) data is stored and accessed by users from their own computer without the large memory requirements. To run the website:
- Activate the environment
- cd into the location of the project
- run
python onedcelltrack/onedcelltrack/webapp/app.py