README

Basic usage

Pre-process and filtering MATLAB

• make_fluo_data.m: Launches the pre-processing of the fluorescent Calcium data with the parameters

• preview_image_stack.m: Crop, rotate, and other basic pre-processing functions. It requires a basic set of parameters.

• process_image_stack.m: Processes the whole image stack according to the predefined parameters. It creates a file with the filtered data and calls the plotting functions when required.

Post-processing and visualization python

• fluo/basic_image_visualization.py: Basic spatial filtering and visualization. Stimulation cycle averaging included.

How do I get set up?

• Get this repo

  • git clone [email protected]:xxx
  • cd hTUS
  • git checkout develop
  • git config pull.rebase false

• To use the python scripts:

  • cd hTUS
  • python3 -m venv venv
  • source venv/bin/activate
  • pip -V
  • python3 -m pip install --upgrade pip
  • pip install scipy
  • pip install matplotlib
  • pip install ipython[all]
  • pip install h5py
  • pip install scikit-image
  • Use deactivate to deactivate the python virtual environment
  • Create a file called fluo_los.sh on your main folder of the pc (or whatever folder where the command window will start) to automate starting python with the following content:

  cd hTUS path
  source venv/bin/activate
  ipython --pylab