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