Introduction to image analysis with ImageJ/Fiji

This page contains the same PDF slides as before.

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

Practice

1. QuPath projects and GUI

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

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

   2. 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?

   3. 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

   1. Recreate the annotations seen in slides

      1. Recommended: use the paint brush tool

      2. Lock your annotations

   2. 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