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:

  • greyscaleGrey scale - the standard black to white mapping for MRI, CT and other images.
  • inverted_greyscaleInverted grey scale - the standard white to black mapping for plain x-ray images.
  • hotbodyscaleHot 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.
  • rainbowscaleRainbow scale - a spectrum of colours.
  • rainbowscale2Rainbow scale 2 - an alternative spectrum of colours.
  • coolCool - the 'cool' spectrum of colours.
  • redscaleRed, greenscaleGreen, bluescaleBlue, yellowscaleYellow, cyanscaleCyan, images/magentascaleMagenta.
  • step_scaleStep - 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:

view_colours

You can also invert the colour scale by selecting the inverted_check check-box towards the bottom of the Colour Scale menu.

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:

view_colour_bar

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.

colour_bar

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
horiz_colour_bar Click for a horizontal colour bar.
vertical_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: colour_bar_screen_shot

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.

You can also show a Colour Bar for an overlaid image by selecting Colour Bar from the View menu of the Overlay Dialog. The Colour Bar shown will correspond to the image set in the currently-selected overlay image tab.

Creating and Importing Colour Mappings

You can also load your own colour mappings into Jim using add_colour_scale 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 delete_colour_scale.

Native Colour Mappings

AnalyzeTM 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 AnalyzeTM 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 AnalyzeTM 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 regardless of where it is displayed. 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.

SMPTE

Then select Display Characteristics ... from the Colours menu. This will bring up the Display Characteristics dialog:

display_characteristics

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 apply_button 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 apply_button button to see the effect of the change.

SMPTE_5_95

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 apply_button button to see the effect of the change. Below is an illustration of what the display looks like for a bad Gamma value:

gamma_too_low

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 set_defaults_button button.

To save the settings so that they will be used next time you start Jim, press the apply_and_save_button button.

Note: 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.
Note: 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 done_button button.