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Welcome to Introduction to Bioimage Analysis using QuPath!
==============================================================

This deck of slides introduces participants to the key concepts of bioimage analysis using the open-source software **QuPath**. It is designed as a primer for biologists who need to analyze images as part of their research but are new to image analysis.

The following materials were developed for a workshop taught in-person at **Harvard Medical School**, organized by the `Image Analysis Collaboratory <https://iac.hms.harvard.edu/>`__.

**Downloadable Resources**
---------------------------

- **Course slides:**
  
  .. raw:: html
  
     <p><a href="_static/all_slides.pdf" download>Download all slides (PDF)</a></p>

- **Whole-slide image materials:**

  .. raw:: html
  
     <p><a href="https://zenodo.org/records/13766331/files/example_image.zip?download=1" download>Download the .vsi whole-slide image (ZIP)</a></p>
  
  Kudos to Nina Kozlova (Muranen Lab, BIDMC, HMS) for providing this example whole-slide image.

**Useful Links**
----------------

Here are some helpful resources to complement the workshop materials:

- `Download QuPath (make sure to install version 0.5x!) <https://qupath.github.io/>`_
- `Download StarDist extension for QuPath 0.5 <https://github.com/qupath/qupath-extension-stardist/releases/download/v0.5.0/qupath-extension-stardist-0.5.0.jar>`_
- `Download "dsb2018_heavy_augment.pb - single channel" StarDist model <https://github.com/qupath/models/raw/main/stardist/dsb2018_heavy_augment.pb>`_
- `QuPath 0.5 Documentation <https://qupath.readthedocs.io/en/0.5/>`_
- `QuPath Discussions on Image.sc Forum <https://forum.image.sc/tag/qupath>`_

**Topics**
------------

Below are the core sections of this workshop, each covering some aspects of bioimage analysis with QuPath.

.. 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


**Feedback**
------------

.. toctree::
   :maxdepth: 1

   08_feedback.rst