BioCampus workshop: What you need to know about QuPath for fluorescence and IHC images analysis

Proposed by Montpellier Ressources Imagerie, 2026

Architecture

• Create your notebooks in the lectures or exercises folder. The content of these folders is automatically converted to HTML.
• Reference them either in the index or in other notebooks so they are reachable.
• The content of media and slides is automatically pushed to the LFS, so you can put your illustrations there (no heavy data).
• You can locally test to build HTML pages using the building instructions (below).

Custom CSS

Insert an input icon

• "Input icon" designates the icons used to indicate what the user should press/click to trigger an action (left click, ctrl+click, ...)
• To do that, an icons pack (CC0) is present in "media"
• To insert an icon use the following markdown:

![Kenney-xxx](../media/inputs-icons/nnn.svg)

• The "Kenney-" prefix is mandatory within the square brackets.
• The "xxx" part is up to you.
• "nnn" is to find in the icons pack folder.

Insert a QuPath icon

• Some QuPath icons are present in "media/qp-icons".
• To insert a QuPath icon use the following markdown:

![QP xxx](../media/qp-icons/nnn.png)

• The "QP " prefix is mandatory within the square brackets.
• The "xxx" part is up to you.
• "nnn" is to find in the QuPath icons folder.

Insert a tip/warning/note block

• Tips, warning and notes must be in their own notebook cell.
• This kind of block is generated using the cell's tags in the IPYNB.
• In VS Code, you can do right-click > "add cell tag" once you are in rendering mode (not cell editing mode).
• Possible values (case sensitive):
  • "tip"
  • "warning"
  • "note"

Build instructions

• Have a Python environment in which nbconvert and beautifulsoup4 are installed, and activate it.
• At the same level as lectures, exercises, ... create a new build directory (don't jump into it).
• Make sure that your terminal's curent directory is the one containing build, lectures ...
• Run the command sh ./build.sh

To-do

• Create a GitHub action to convert the slides to PDF.
• Write the installation tutorial for all requirements.