towbintools 0.3.3

All the tools used by the Towbin Lab !

towbintools!

This is the package containing all the important functions used by the Towbin Lab of the University of Bern. Most of the code is a python translation of our old Matlab pipeline.

Documentation : https://towbintools.readthedocs.io/en/latest/towbintools.html

Deep learning

This package uses the pretrained-microscopy-models package (available here : https://github.com/nasa/pretrained-microscopy-models/tree/main) which is not available as a pip dependency. If you want to use the deep learning part, you will have to install it using:

pip install git+https://github.com/nasa/pretrained-microscopy-models

Setting up a Virtual Environment

Using a virtual environment isolates your package dependencies and settings from your system Python. Here's how you can set one up:

1. First, create a folder where the venv will be stored:

   mkdir ~/env_directory
   

2. Create the venv:

   python3 -m venv ~/env_directory/towbintools
   

3. To activate the venv:

   source ~/env_directory/towbintools/bin/activate
   

4. Whenever you are done working, you can deactivate it with:

   deactivate
   

How to add a python venv to Jupyter

1. First, make sure Jupyter and related packages are installed:

   pip3 install jupyter ipykernel
   

2. Add your venv to Jupyter:

   python3 -m ipykernel install --user --name=towbintools
   

3. If you're using VSCode, reload VSCode and you should be able to find the kernel.

Install the package using pip

Simply run the following command:

pip3 install towbintools

Build the package and install it

1. First, make sure build is installed:

   pip3 install build
   

2. Go to the package directory, eg:

   cd ~/towbintools
   

3. Build the package:

   python3 -m build
   

4. Install the package you just built:

   pip3 install dist/*.whl
   

You're now all set!