Image Dimensions

Image Dimension Display

Whenever an new image is loaded into Jim, the image loader attempts to determine the physical size of the pixels (in mm). In UNC format images, these come from the "Info Fields":

pixel_x_size for the width of a pixel.
pixel_y_size for the height of a pixel.
pixel_z_size or slice_thickness for the depth of a pixel.

In Analyze™ and NIFTI-1 format images, the pixel dimensions are set in the image header. These dimensions are used by Jim to display dimensions, and to calculate areas and volumes.
Note: if Jim cannot find the pixel dimensions when it loads an image, then it displays a warning message, and sets the size of a pixel to 1.0 mm.

Switching Between Pixels and mm

The dimensions of displayed image objects can be displayed either in pixels or in millimetres (mm).

When dimensions are displayed in mm, you will see a button like: in the top left of some windows.
When dimensions are displayed in pixels, you will see a button like: in the top left of some windows.

Click either button to toggle between display in pixels or mm.

Coordinate System

The coordinate system when image dimensions are shown in pixels is:

Pixel coordinates are always shown in integer values of pixel number. Pixel (1,1) is at the top left of the image, and the column and row number increase to the right and downwards respectively.

The coordinate system when image dimensions are shown in millimetres is:

The origin (0,0) is at the centre of the field-of-view, and the x and y values increase to the right and downwards respectively.

Dimension Display

As you move the mouse over the image, the dimension display towards the bottom of the display window will show the position of the cursor, and the image intensity under the cursor.

The things shown in the dimension display are:

The slice number under the mouse. Slices are numbered from 1 to the number of slices in the data-set.
The x- and y-coordinates of the cursor relative to the image slice. This can be either in pixels or mm.
The image intensity under the mouse.

Note: when the displayed image is an R,G,B image, the intensity displayed is the luminance value of the pixel, where luminance is defined as:

0.299 Red + 0.587 Green + 0.114 Blue

Where Red, Green and Blue are the red green and blue gun values.

Note: when the displayed image is a complex image, the intensity displayed depends on the complex display mode.

If a movie is running, then the image intensity is continuously updated as the movie steps through the frames.

Storage of Dimensions

Whenever image dimensions are saved to disk (for example, as part of the definition of a Region of Interest, the coordinates of the outline are stored), they are stored in mm rather than pixels. This ensures that if these dimensions are loaded into other images (for example, when a Region of Interest is loaded into another image), the dimensions are independent of the pixel size and field of view in the two images.

Note: it is assumed that pixel sizes are specified in millimetres in the image files.

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