1. Install dependencies.

• OSX/Windows You will probably want to install Anaconda, a Python package manager. IMPORTANT: Install the Python 3.X version.

• Linux You will need Python 3, and the python3 packages numpy, matplotlib, and pillow, installed through your package manager or pip.

2. Clone this repository.

• Open the terminal, and run git clone git@github.com:wackywendell/diffusiontrap.git

That's all, there's no setup for a pure-python program like this.

1. Export your data.

• First, you will need to export your data to tif format, so that it alternates yellow and cyan frames, with cyan first.

2. Open a terminal in the right directory.

• Open the Terminal application.

• Type in cd /Users/your_username/directory_you_want_to_work_in

• Run python3 /path/to/diffusiontrap.py path/to/image.tif

3. Choose your options.

• Run python3 /path/to/diffusiontrap.py --help to see all the options

• For example, run python3 /path/to/diffusiontrap.py -t 20 -u 150 to use a threshold of 20 and an "upper limit" of 150.

4. Files will appear in the same directory as the original image, with roughly the same name as the original file.

• The one ending in .csv is the spreadsheet with all the columns.