Introduction to image analysis with ImageJ/Fiji
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This page contains the same PDF slides as before. 

.. raw:: html

   <iframe src="_static/01_intro_digital_image_analysis.pdf" width="100%" height="600px"></iframe>


Below is an example on how to list exerices for the course:

**Practice**
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1. QuPath projects and GUI

   a. Change LUT colors of the channels (Brightness & Contrast tab)

      1. DAPI = blue, FITC = green, TRITC = red, CY5 = yellow

   b. LUT, Brightness & Contrast and pixel values

      1. Select one of the channels for display
      2. Zoom into the image to inspect the value of a single pixel, and note its value
      3. Adjust the Brightness & Contrast, and the LUT range (min/max)

         - How did the pixel value change?

      4. Change the LUT to grayscale or any other color
      
         - How did the pixel value change?

   c. Multi-viewer

      1. Use the command list (Command/CTRL + L) to find the command to add a second display window to the default window
      2. Display one channel in each viewer window
      3. Zoom in and out, then export snapshots (make sure to include a scale bar)

2. QuPath manual annotations

   a. Recreate the annotations seen in slides

      1. Recommended: use the paint brush tool
      2. Lock your annotations

   b. Create an annotation to circle a region of interest (ROI)

      1. Circle a region of high signal intensity in the fibronectin channel
      2. Lock your annotation
      3. Optional: rename it