Lab Contents

Introduction to Image

(Differences between Scion Image 1.61 and NIH Image 1.61 are shown in magenta.  Notes specific to ImageJ are shown in green.  For an introduction to ImageJ, please see the ImageJ web site. In a way, ImageJ is simpler - the only window that opens upon starting the program is this: 

 Upon starting the application, no image will be shown. Images are shown when you open them with the File menu, drag an image onto NIH Image, or double click on an image that is 'registered' as an NIH (Scion) Image document.

The Info window initially appears blank. Clicking the middle of the line in the Map window and moving it a bit (arrow a) shows the upper and lower limits (a) (Scion Image - limits not shown). Clicking on the Info window title bar (c) will show the Count, area, mean (zero becaure there is no image yet)(Scion Image - these three as yet meaningless parameters are not shown). Moving the mouse in the LUT (arrow b) will show the intensity level and the colors assigned to it.

Set units to pixels with Analyze -> Set Scale... menu. Don't leave units as 'arbitrary.'


Colors in Image

In b above, why are the RGB colors 206 for an index of 109? Two reasons: in Image (for historical reasons - I believe Image was initially developed to analyze gel chromatographs, where the background is light and stains are dark), low pixel values are white and high pixel values are black. The second reason is that the line in the Map bar was moved.

 Clicking on the reset button (arrow) in the Map window resets the line (and the gray level bar in the LUT window).  

Then moving the cursor (it looks like the eye-dropper when over the LUT window) to the arrow (right) shws this in the Info window: 

For gray level images (such as this gray level ramp), the red, blue and green components are the same.

The Index and the intensity level sum to 255. Note - Index 0 has a level of 255, and index 255 has a level of zero.



Images are shown in windows that can be moved about indepently about on the screen. The tool windows can also be moved - by dragging the title bar. There is only one IMAGE window that is in the front or active at any one time. The title bar of the active image winow will be noticably different from the others.


Tools affect how the cursor appears, and what clicking and dragging will do.

Most of these tools are in ImageJ.

 This diagram of the Tool window is from the NIH Image Manual.