Crop image and add scale bar with ImageJ/Fiji

imagej
Author

Guorui Zhong

Published

Tuesday, March 16, 2021

Crop images to a given physical size

  1. Edit -> Selection -> Specify
  2. image -> Crop

Crop same area from different images

  1. Select the area on the first image
  2. Analyze -> Tools -> ROI manager -> Add [t]
  3. Click the second image, select and click the parameters on the ROI manager

Set scale and add scale bar

  1. Analyze -> Set Scale

  • Nikon (20x object):

    • 3.2 pixel/um, 5 um/16 pixel
    • 5uM = 16 pixels (cellxpress exported as 100%)
    • 5uM = 32 pixels (cellxpress exported as 200%)
    • 5uM = 64 pixels (cellxpress exported as 400%)
    • 12.8 pixel/um (when exported with 400% zoom in using cellXpress)

  • Nikon (40x object):

    • 6.25 pixel/um, 0.16 um/pixel
    • 1um = 6.25 pixel (cellxpress exported as 100%)
    • 1um = 12.5 pixel (cellxpress exported as 200%)
    • 1um = 25 pixel (cellxpress exported as 400%)
    • 5uM = 125 pixels (cellxpress exported as 400%)

  • TC microscope:

    • physical length of a pixel: 3.4375 um
    • 10x: 0.34375 um/pixel = 2.91 pixel/um
    • 20x: 0.171875 um/pixel = 5.82 pixel/um

  1. Analyze -> Tools -> Scale bar

  2. File save as png format.