Cell Tracking

Download slides (Optional)

All the slides that will be used in this session are here.

Download demo data

We’re going to be working with some example datasets, which you can download from here.

Set up conda environment

For this module, you need to set up a conda environment to analyse tracking data in Jupyter notebooks.

1. Make sure you first installed conda properly by following these instructions.
2. Make sure you have already downloaded all the scripts we will be using by clicking on the tar or zip icon on this page.
3. Open Anaconda Prompt (use terminal on Macs) and navigate to wherever you saved and unzipped the scripts in step #2 above:

    cd <path_to_unzipped_files>/FrancisCrickInstitute-multi-dimensional-imaging-and-analysis-*******/Live-Cell-Imaging-And-Tracking
   

   You’ll need to replace <path_to_unzipped_files> with the location of the unzipped folder on your computer.

4. Type the following to create a new environment:

    conda create --name cell-tracking python=3.13
   

5. Check that the environment was created:

    conda env list
   

6. Activate your new environment so you can use it:

    conda activate cell-tracking
   

7. Install the necessary packages for this session:

    python -m pip install -r ./tracking_requirements.txt
   

8. Open Jupyter Lab:

    jupyter-lab
   

For more information on using conda, see here.

For a detailed explanation on Jupyter Lab, visit the Jupyter Lab User Documentation

Run the Jupyter notebooks on Binder

Binder allows you to open notebooks stored in a GitHub repo in a remote executable environment, making your code immediately reproducible by anyone, anywhere.