Running notebooks locally

The short version

In order to run ZeroCostDL4Mic notebooks locally, it is important to ensure that the correct packages are installed. We recommend creating a new Conda environment on your local machine for every notebook that you intend to use and installing the required packages with pip from a requirements file.

For instance, to create a Conda environment to run the 3D U-Net notebook locally follow these steps:

1. Open a notebook in Google Colab from the wiki page and import the required packages

2. Download requirements.txt from the Files tab located in the upper left corner of the Google Colab notebook

3. To create a new Conda environment on your local machine, run $ conda create -n myzerocostenv python=3.6.9 in the terminal
4. Next, activate your new environment by running $ conda activate myzerocostenv
5. To install the necessary packages navigate to the location of requirements.txt and run $ pip install -r requirements.txt
6. Let us know if you encounter any issues and enjoy ;)

How to connect Google Colab to a local runtime

These tutorials were written by Seyed Hosseini and funded by Abo Akademi University's "Open Science" initiative.

Video tutorial	Text-based tutorial

How to modify a ZeroCostDL4Mic notebook so that it can run locally

(coming soon)