d-v-b/tutorial

image analysis and visualization in Python with scikit-image, napari, and

friends

A SciPy 2023 tutorial

See the tutorial page on the SciPy 2023 site for details.

installation

⚠️ WARNING: You should reinstall this just before the conference as we might have made some changes by then. ⚠️

You can install the requirements for this workshop in two ways:

using conda/mamba

To use conda or mamba, use the provided environment.yml file. For example:

conda env create -f environment.yml

then:

conda activate image-analysis-23

using your own environment manager

If you want to install into your own environment (as a reminder, never install to your operating system's system-wide Python install; if you don't know what this means, use conda as described above), you can use:

python -m pip install -r requirements.txt

Checking that your installation works

If you have installed everything correctly, you should be able to run:

python test-env.py

Some of the libraries take a while to run the first time, so be patient. You should see (1) a matplotlib window with three image panels pop up; when you close this, (2) a napari window showing the same coins image should show up. When you close this, the script should finish without errors.

Running this workshop

This workshop uses .md files to represent jupyter notebooks managed by jupytext. Once you have installed jupytext (as per the instructions above), the experience should be the same as using a regular Jupyter notebook: launch jupyter notebook or jupyter lab, go to the "notebooks" folder, and click on each notebook as instructed by the tutors.