Training materials for python/napari workshops
There is a mixture of Python experience among the attendees. In order to plan a training session that I hope everyone will benefit from, before the session please can you:
- Everyone: Download and unzip the attached zip folder (make sure you know where you've saved it)
- Beginner Python users: I recommend installing Anaconda. After installing please follow the step by step instructions in AnacondaSetup.pdf.
- Experienced Python users: Set up a virtual or conda environment with Python 3.9 or above. Within the environment please install napari (I use python -m pip install napari[all], check the instructions for your operating system if you have issues). Also install matplotlib. I will be using jupyter notebooks on the day, so if you'd like to follow along with me, please install jupyter notebook. However, if you'd rather use your favourite IDE that should be fine too. After activating the environment, please check you can run the SetupCheck.py script (or SetupCheck.ipynb if using jupyter notebook) from the attached .zip folder.
You should get a Napari window that opens and looks like the picture SetupCheck.png. If you do not, please email me so I can help! There will not be time to troubleshoot the setup during the training session, you can still attend the training, but will not be able to follow along with the coding. You are welcome to use your own images during the training session if they are in .tif format.
To learn more about image analysis with python, take a look at Neubais bioimage analysis with python course