Colour Mapping
The colour mapping converts image intensity values (which are just
numbers) into displayed colours on the screen. Jim
has several built-in colour mappings:
Grey scale - the standard black to white mapping
for MRI, CT and other images.
Inverted grey scale - the
standard white to black mapping for plain x-ray images.
Hot body scale - the scale
representing intensities as "temperatures" from black (cold)
to white (hot) with various colour in between that would be
seen on heating a black metal to white hot.
Rainbow scale - a spectrum of colours.
Rainbow scale 2 - an alternative spectrum of colours.
Cool - the 'cool' spectrum of colours.
Red, 
Green,
Blue, 
Yellow,
Cyan, 
Magenta.
Step - all pixels above the mid brightness
setting are shown white, and all those below are shown black.
You can change the colour mapping from the View menu, Colours item:
You can also invert the colour scale by selecting the
check-box.
The Colour Bar
You can show the colour scale that maps pixel intensity values
to colour on the image in the form of a colour bar. To show the
Colour Bar, select Colour Bar from the View menu:
This pops up a colour bar, initially in a vertical
orientation. The scale along the side of the colour bar shows the
pixel intensity value corresponding to an pixel colour: as you
change the contrast adjustment, the colour bar is updated to show the
new mapping.
A colour bar for the Rainbow 2 colour scale, in a vertical orientation.
You can flip between a vertically- and horizontally-orientated
colour bar by clicking on the icons at the top of the Colour Bar
frame.
Colour Bar Orientation Buttons
 |
Click for a horizontal colour bar. |
 |
Click for a vertical colour bar. |
You can create a picture of the colour bar on disk, for inclusion in
illustrations, by selecting Screen shot ... from the
File menu of the Colour Bar: 
A dialog will pop up asking
for the format of the picture (JPEG, GIF etc.) and then a further File Chooser dialog so that you can set the
file name for the colour bar image.
Creating and Importing Colour Mappings
You can also load your own colour mappings into Jim using
in the colour scales menu.
This will bring up a File Chooser for you to select a file
that defines the colour scale. The file can be:
- In binary format. The file must be 768 bytes long and must contain the red,green,blue
[R,G,B] gun values in binary format as unsigned byte values. There must be 256 gun values
and all the red gun entries must be followed by all the green, which must be followed by the
blue entries. This binary format is also used by
ImageJ.
- In text format. The file must contain 256 entries with each entry being a triplet of
red,green,blue gun values between 0 and 255, with the [R,G,B] values interleaved.
Typically, the [R,G.B] entries will be presented in 3 columns and 256 rows of numbers.
Once the [R,G.B] entries have been read from the file, you will be prompted for a name for the
colour mapping, and the colour mapping will appear with this name in the menu of available
colour mappings.
User-defined colour mappings can be deleted from the menu be selecting 
.
Native Colour Mappings
Analyze™ images can have their own colour mappings (called lookup
tables) - stored in a file with extension ".lkup". If Jim
detects one of these colour mappings while loading an
Analyze™ image, it will automatically load it. The colour mapping
will then appear in the Colours menu item as Native colour
scale, since it is "native" to the loaded image. Unless an
Analyze™ image with a corresponding ".lkup" file is loaded,
this menu item is greyed out.
UNC images may also have a native colour mapping that is stored in
the image header, in an info field with a name
"Colour_Mapping". If Jim detects this info field, it will
load the colour mapping as the native mapping.
DICOM Standard Grayscale Display
The latest DICOM standards specify a way of setting up a computer
display so that the same medical image will be perceived
to have the same image contrast and brightness. Setting up a
display in exact compliance with the DICOM standard is
time-consuming and requires the use of expensive test equipment
that is not readily available. However, Jim provides a simple way to
set up you computer display that will correct any major
differences in your display setup. The setup will take account of:
- The ambient lighting conditions of the room in which Jim
is used. For this reason, always make these adjustments under
normal ambient lighting conditions.
- The maximum luminance of the display screen.
- The gamma value for your display screen.
To setup the display, first load the SMPTE test card. This is
provided in the set of example
images that can be downloaded when you
installed Jim.
Then select Display Characteristics ... from the
Colours menu. This will bring up the Display
Characteristics dialog:
Now concentrate on the central lower portion of the test card. The
squares shown below contain smaller squares that are slightly
brighter than (on the left) and slightly dimmer than (on the
right) their surrounding squares.
- Adjust the Min. luminance value until the brighter square on
the left is just visible inside the outer square. This
adjustment takes account of room ambient lighting
conditions. Click on the
button to see
the effect of the change.
- Adjust the Max. luminance setting until the darker square on
the right is just visible inside the outer square. This
adjustment takes account of the maximum brightness of your
computer display. Click on the button to see
the effect of the change.
The final setting is the gamma correction for your monitor. Adjust
the gamma value until you perceive that there is a constant step
in brightness from one square to the next as you move around the
square of grey tones from the black square to the white square.
Click on the button to see
the effect of the change.
Below is an illustration of what the display looks like for a bad
Gamma value:
In the picture above, all the low grey values are dark, and there is
very little difference in contrast between these squares. In this
case, the Gamma value is set too low. If, on the other hand, the
Gamma value is set too high, then the bright tones will appear
washed out, with little difference in contrast between the bright
squares. If in doubt, the default setting (2.6) will be about right for
most computer displays.
To revert to the default setting for your display
characteristics, press the 
button.
To save the settings so that they will be used next time you start
Jim, press the 
button.
N.B. The display characteristics setting are saved in the
user's preferences for each computer that the user sets up. The
procedure for setting up the display should be followed for every
computer that the user logs on to.
N.B. If the ambient light conditions change significantly, or the contrast and
brightness settings for the computer monitor are changed, then
the display characteristics should be set up again using this procedure.
When you have finished setting up the display characteristics,
click the 
button.