.. QuPath documentation master file, created by
   sphinx-quickstart on Fri May 24 09:11:52 2024.
   You can adapt this file completely to your liking, but it should at least
   contain the root `toctree` directive.


Introduction to Bioimage Analysis using QuPath
==================================================

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 busy 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 <https://iac.hms.harvard.edu/>`__.

**Download the course materials:**

.. raw:: html

   <p>1. Slides: <a href="_static/all_slides.pdf" download>Download PDF</a></p>

Contents
=======================================

.. toctree::
   :maxdepth: 1

   01_intro_image_analysis.rst
   02_intro_qupath.rst
   03_qupath_projects_and_GUI.rst
   04_cell_detection.rst
   05_cell_classification.rst
   06_tissue_annotation.rst
   07_scripting_workflows.rst