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1 | 1 | # SYWTDIAWP |
2 | | -So You Want To Do Image Analysis With Python |
| 2 | + |
| 3 | +So You Want to Do Image Analysis with Python. |
| 4 | + |
| 5 | +This repository hosts a GitHub Pages course for biological researchers learning |
| 6 | +to work with Python locally for image analysis and related workflows. |
| 7 | + |
| 8 | +The course is paced as a multi-day self-study resource rather than a short |
| 9 | +single-session workshop. |
| 10 | + |
| 11 | +The current course covers: |
| 12 | + |
| 13 | +- installing Python locally |
| 14 | +- working with virtual environments using `venv` and conda |
| 15 | +- learning core Python programming basics such as variables, data types, and functions |
| 16 | +- learning the main scientific Python libraries used in research |
| 17 | +- running Jupyter notebooks |
| 18 | +- using pandas and matplotlib for tabular data and plotting |
| 19 | +- installing napari and launching the `napari-mAIcrobe` plugin |
| 20 | +- creating a Python package from the HenriquesLab cookiecutter template |
| 21 | +- continuing into segmentation, classification, QC, neural networks, and pretrained models based on the BioimageCourseGIMM notebooks |
| 22 | + |
| 23 | +## Structure |
| 24 | + |
| 25 | +- `index.html` is the landing page and course map |
| 26 | +- `resources.html` is the central resource hub for notebooks and quick links |
| 27 | +- `glossary.html` contains beginner-friendly definitions for recurring terms |
| 28 | +- `troubleshooting.html` collects common setup and workflow recovery steps |
| 29 | +- `404.html` is the fallback page for broken GitHub Pages links |
| 30 | +- `assets/css/site.css` contains the shared site styles |
| 31 | +- `tutorials/install-python.html` covers local Python installation |
| 32 | +- `tutorials/virtual-environments.html` covers `venv` and conda |
| 33 | +- `tutorials/python-basics.html` covers Python fundamentals and exercises |
| 34 | +- `tutorials/scientific-python-libraries.html` introduces the main scientific Python tools |
| 35 | +- `tutorials/jupyter-notebooks.html` covers notebook setup, examples, and exercises |
| 36 | +- `tutorials/pandas-and-matplotlib.html` covers tabular analysis and plotting |
| 37 | +- `tutorials/napari-maicrobe.html` covers napari and `napari-mAIcrobe` |
| 38 | +- `tutorials/create-python-package.html` covers package creation with cookiecutter |
| 39 | +- `tutorials/advanced-*.html` pages extend the same course path with BioimageCourseGIMM-inspired lessons |
| 40 | +- `notebooks/` contains sample notebooks linked from the Jupyter lesson |
| 41 | + |
| 42 | +## Publishing With GitHub Pages |
| 43 | + |
| 44 | +Because the site is plain HTML and CSS, it can be published directly from the |
| 45 | +repository without a build step. |
| 46 | + |
| 47 | +1. Push the repository to GitHub. |
| 48 | +2. In the repository settings, open `Pages`. |
| 49 | +3. Set the source to deploy from the `main` branch and the repository root. |
| 50 | +4. Save the settings and wait for GitHub to publish the site. |
| 51 | + |
| 52 | +## Local Editing |
| 53 | + |
| 54 | +You can edit the HTML files directly and refresh them in a browser, or run a |
| 55 | +simple local server from the repo root: |
| 56 | + |
| 57 | +```bash |
| 58 | +python -m http.server 8000 |
| 59 | +``` |
| 60 | + |
| 61 | +Then open `http://localhost:8000`. |
| 62 | + |
| 63 | +## Content Notes |
| 64 | + |
| 65 | +- The lesson pages are written for researchers who may be new to programming. |
| 66 | +- Commands are intentionally copy-paste friendly and organised as a guided path. |
| 67 | +- The modules now include slower pacing, checkpoints, and suggested stopping points. |
| 68 | +- If the HenriquesLab cookiecutter repository path changes, update the command |
| 69 | + in `tutorials/create-python-package.html`. |
| 70 | +- The public site navigation now points to HTML pages rather than raw Markdown |
| 71 | + files so the GitHub Pages experience stays consistent. |
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