1 - Working with Single-Channel Images

1 - Working with Single-Channel Images#

1.1 - Image inspection#

  1. open the single_channel.tif image (drag & drop, or File > Open)

  2. Image > Duplicate (IJ:28.9) (shift + d)

  3. Analyze > Histogram (IJ:30.10) (h)

  4. click Live

  5. Image > Adjust > Brightness/Contrast (shift + c)

    • play with Maximum, Minimum, Brightness and Contrast sliders and with Auto, Set and Reset

    • observe the histogram window, what is changing, what is not?

    • click Apply

    • what changed?

1.2 - Adjust brightness/contrast of all open images#

  1. open the three single_channel_...tif images in folder for_exercise_1.2 (drag & drop, or File > Open)

  2. for all images: Analyze > Histogram (IJ:30.10) (h)

    • click Live

  3. for one image: Image > Adjust > Brightness/Contrast (shift + c)

  4. adjust contrast with Maximum, Minimum, Brightness or Contrast sliders or Auto

  5. click Set

  6. check Propagate to all other open images checkbox

  7. click OK

  8. what happened to the histograms?

  9. what happened to the images?

  10. did pixel values change?

  11. pick another image and repeat steps 4–7

  12. what happened, what is different, is it better/worse?

1.3 - File handling and non-invasive editing#

  1. File > Open Samples > Blobs (IJ:26.4) (shift + b)

  2. Analyze > Tools > Scale Bar (IJ:30.14.6)

    • set Color, Background, Location

    • check: Overlay, Bold Text

  3. File > Save As > Tiff -> blobs1.tif (IJ:26.10.1)

    • saving the image as tiff keeps the scale bar as an overlay, so pixel values below it are kept

    • NOTE: you can see the ovarlay scale bar in the saved image only if you open it in Fiji

    • continue with 1.4

1.4 - File handling and invasive editing#

  1. open the blobs1.tif saved in 1.3 (drag & drop, or File > Open)

  2. Image > Info (IJ:28.3) (i)

  3. Image > Overlay > Remove Overlay (IJ:28.14.7)

    • the scale bar should disappear since it was saved as an overlay

  4. Analyze > Set Scale (IJ:30.8)

    • set scale such as image is 100 um long in each dimension

  5. Analyze > Tools > Scale Bar (IJ:30.14.6)

    • set Color, Background, Location

    • uncheck Overlay

  6. File > Save As > Tiff -> blobs2.tif (IJ:26.10.1)

  7. load again to check the difference (e.g. check info, hover over the scale bar and look at the pixel values)