Maloof Lab:ImageJ Time Lapse Hypocotyls

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Room 2115
Section of Plant Biology
1002 Life Sciences, One Shields Ave.
University of California Davis
Davis, CA 95616


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  1. Open the images in ImageJ
    1. Launch ImageJ
    2. Choose File>Import>Image Sequence
    3. For manual measurement 30 minute time lapse is good. If you have more images than this you can import a subset by setting the increment to something > 1
  2. Crop and rotate the stack as necessary using the tools in the Image menu
  3. Set up measurements and scale
    1. Check the "stack position" box in Analyze>Set Measurements in imageJ. Uncheck everything else.
    2. Set scale based on first image (use "SetScale..." in the "Analyze" pull-down menu).
    3. Select the segmented line tool from the toolbar (right click on the straight-line selection tool)
  4. Click along the first hypocotyl in the first slice
  5. Press "M" and then ">" (you do not need to hold down a modifier key, at least on the Mac, even though it says that you need to press the command key)
  6. Adjust the selection (measurement line) to fit the hypocotyl on the next slice by dragging the "handles".
  7. Repeat the previous two steps until you are though all of the images
  8. Paste the data into excel
  9. Repeat the last 5 steps for the next hypocotyl