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Welcome to Introduction to Bioimage Analysis using ImageJ/Fiji! 
===================================================================

This set of slides introduces participants to key concepts in bioimage analysis using the open-source software **ImageJ/Fiji**. It is designed as a primer for biologists who need to analyze images as part of their research but are new to image analysis.
This course also stresses out the importance of reproducibility and quantiative image analysis in biological research.

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>

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

- **Course images:**
  
  .. raw:: html
  
     <p><a href="_static/images/images.zip" download>Download all images (ZIP)</a></p>


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

Here are some helpful resources to complement the workshop materials:

- `Download Fiji <https://fiji.sc>`_
- `ImageJ/Fiji documentation <https://imagej.net/ij/docs/index.html>`_
- `The Forum <https://forum.image.sc/>`_


**Topics Covered**
-------------------

Below are the core sections of this workshop, each focusing on different aspects of bioimage analysis using ImageJ/Fiji.

.. toctree::
   :maxdepth: 1

   01_intro.rst
   02_intro_to_fiji.rst
   03_thresholding.rst
   04_filtering.rst
   05_labkit.rst
   06_morphology.rst
   07_segmentation_measurements.rst
   08_spot_detection.rst
   

**Exercises**
---------------

.. toctree::
   :maxdepth: 1

   exercises.rst
   images.rst


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

.. toctree::
   :maxdepth: 1

   feedback.rst