This work is licensed under a Creative Commons Attribution 4.0 International License.

QuPath workshop at Harvard Medical School

This deck of slides introduces participants to the main ideas of bioimage analysis using the open-source software QuPath. It is designed as a primer on QuPath for biologists who need to analyze images part of their research. These materials were initially designed for a workshop taught in-person at Harvard Medical School - organized by the Image Analysis Collaboratory.

Update materials with Sphinx

This repository uses Sphinx to generate documentation from reStructuredText (reST) files. Typically, one would simply modify the slides and replace the relevant file in docs/source. Then, file paths have to be updated in the documentation as described below.

Getting started

To modify the content of this repository, follow these steps:

1. Clone the repository: Clone this repository to your local machine using Git.

   git clone https://github.com/HMS-IAC/qupath-workshop.git

2. Create an environment: For example, using conda.

   conda create -n iac-qupath-workshop python=3.10
   conda activate iac-qupath-workshop

3. Install Sphinx: If you haven't already installed Sphinx, you can do so using pip. furo is the Sphinx theme used.

   pip install sphinx pydata_sphinx_theme sphinx_copybutton sphinx-multiversion

4. Navigate to /docs: Navigate to the directory containing the documentation source files.

   cd docs

5. Modify and build for as single version: Edit the .rst files in the source directory to make changes to the documentation content. You can use any text editor to modify these files. Then, build the html files.

   make clean

   make html
   ```: 
   

6. Build multiple versions with sphinx-multiversion: The sphinx-multiversion extension allows control versions across github branches. The materials for an edition should be contained in its own branch. This extension will build the html files for each branch and version. It is recommended to run this command from the root directory of the main branch, and keep a gh-pages branch clean for page publication.

   cd docs
   make clean
   cd ..
   sphinx-multiversion docs/source/ docs/build/html 

7. HTML files: After building the documentation, you can view the updated the HTML files located in the docs/build/html directory.

8. Move the content of docs/build/html to root directory of gh-pages branch: use a tmp folder, and drog and drop the folders (each folder contains the materials of a version) to the root of the publishing branch.

9. Commit and Push Changes: After verifying that the documentation looks as expected by opening local html file, commit your changes and push them to the repository.

   cd ..
   git add .
   git commit -m "Update documentation"
   git push

Additional resources

• Sphinx Documentation: Official documentation for Sphinx.
• reStructuredText Primer: Learn the basics of reStructuredText (reST) markup language.