whole_AL_segmentation

To install all the appropriate python packages, please type the following on the command line:

mamba create -n caiman -y anaconda::scikit-image conda-forge::caiman numpy seaborn pandas matplotlib

Then navigate to the main directory of this github repo and type on the command line:

pip install -e .

If you find that running 01_segment_and_extract_traces.ipynb takes a long time, you can run the following command:

jupyter nbconvert --to script 01_segment_and_extract_traces.ipynb

which converts the notebook to a python script. You can then submit a job that runs this script via run.sh.

The notebook 01_segment_and_extract_traces.ipynb creates two subdirectories:

• binary_mask_plots: stores 2D projections of the binary mask that is used to compute mean fluorescence over time
• results: stores csv files of the extracted signals that can be loaded into DataFrames for downstream analyses