Maloof Lab:ImageJ Time Lapse Hypocotyls


 * 1) Open the images in ImageJ
 * 2) Launch ImageJ
 * 3) Choose File>Import>Image Sequence
 * 4) 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
 * 5) Crop and rotate the stack as necessary using the tools in the Image menu
 * 6) Set up measurements and scale
 * 7) Check the "stack position" box in Analyze>Set Measurements in imageJ. Uncheck everything else.
 * 8) Set scale based on first image (use "SetScale..." in the "Analyze" pull-down menu).
 * 9) Select the segmented line tool from the toolbar (right click on the straight-line selection tool)
 * 10) Click along the first hypocotyl in the first slice
 * 11) 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)
 * 12) Adjust the selection (measurement line) to fit the hypocotyl on the next slice by dragging the "handles".
 * 13) Repeat the previous two steps until you are though all of the images
 * 14) Paste the data into excel
 * 15) Repeat the last 5 steps for the next hypocotyl