Plant Physiology

Plant Physiology (Biology 327) - Dr. Stephen G. Saupe; College of St. Benedict/ St. John's University; Biology Department; Collegeville, MN 56321; (320) 363 - 2782; (320) 363 - 3202, fax; ssaupe@csbsju.edu

ImageJ

This program is a Windows version of the popular program, NIH Image that was originally written for the Macintosh. ImageJ allows you to make measurements of images and once the measurements are completed, the images can be stacked and made into a movie.

I. Source:
ImageJ is freely available from the NIH. To use ImageJ you can:

Download it for free to your personal computer by going to the NIH website. Once you download the program to your M drive you will need to "unzip" it. Follow the directions provided; or
Run the program on your computer as an applet. To do this, you will first need to set your internet browser to accept the NIH website as a "Trusted Sites Zone." To do this using Microsoft Internet Explorer follow the instructions provided at the NIH web site:

Go to the Tools/Internet Options... dialog
     Select the "Security" tab
        Select the "Trusted sites" icon
           Click "Sites..."
              Uncheck "Requires server verificaton..."
              Add "http://rsb.info.nih.gov" to "Web Sites:"
              Click "OK"
           Click "Custom Level:"
              Under Microsoft VM/Java permissions, check "Custom"
              Click "Java Custom Settings"
                 Select "Edit Permissions" tab
                 Under "Unsigned Content"/"Run Unsigned Content", make sure
                   "Run in sandbox" is checked and then check all the "Enable"
                    buttons under "Additional Unsigned Permissions"
                 Click "OK"
              Click "OK"
           Click "OK"

ImageJ should, running under IE 5, now be able to read and write local files, print, and copy text to the system clipboard.

II. Using Image J to animate a series of images

Open ImageJ. (if you run the program from your computer don't move the ImageJ icon to your desktop, it won't work. Leave it in the directory in which you unzip the ImageJ files).
Select File, Import, Image Sequence
Open the directory in which you have stored your images. Click on the first image and then "OK".
This will read your files into a stack. You can click on Image/Stacks/Animate to see how it will look as a movie. Click inside the movie to stop the animation. You can also change the animation speed.
To create a movie from the images, select File, Save As, Avi. Then, give it a name. This movie can be played by Windows Media Player or other programs.

III. Making measurements with ImageJ.
One advantage of ImageJ (and NIH Image) is that this program allows you to make measurements directly from the images. For example, ImageJ will easily measure line length, angles, perimeter and area. You can calibrate your measurements to record the units in "real" units. It is also possible to compare images with one another by using the Image Math command. This is helpful when comparing two images. To take advantage of these features, consult the documentation with ImageJ. To make measurements of the images that will be in your movie:

Select Image, Stacks, Convert Stacks to Images. This will open each image separately (to convert them back to a stack, select Image, Stacks, Convert Images to Stacks)
Then select the tool you want to use (e.g., angle). Click the tool on the angle to measure, then select Analyze, Measurement.

IV. Using Image J to Make a Montage of Images and a Flipbook.
ImageJ will allow you to print a page with a series of images (a montage) or to make a flipbook (remember them from your childhood). To do this:

Assume you have a series of 20 images you want to print as a montage. Convert the images to a stack (File, Acquire, Stack)
Under the 'Image' menu, select 'Stacks'.
Then set 'First Slice' to 1 and the 'Last Slice" to 20. Set the increments to 1. The 'Column', 'Row' and 'Size Factor' will self adjust to print your images on a single page.
Turn the 'Number Slices' off and the 'Borders' on.
The resulting image will be a montage of 20 images in numerical order suitable for printing out.
The images can be cut out, glued to sheets of stiff paper, stapled at the margin, and then used to create a flipbook.