Thursday, 13 March 2014

Regarding calibration in the dicom image using ImageJ

1. I assume you have these in DICOM format. In ImageJ it is simple to import a single DICOM image and the calibration is done for you (the DICOM header contains fields for slope and intercept (usually 1 and -1024)). Since you have a stack this is probably not much good. For importing tomographic studies I use the "Import Dicom sequence" plugin available here:

From what I remember it is not the most straight-forward plugin to install but will nicely import a sequence of DICOM images as a stack. It does not, however, seem to calibrate the gray levels into hounsfield units. To do this choose Analyse->Calibrate. Choose "Straight line" as the function, type -1024 in the left box and 0 in the right box. When you press OK you get a straight-line graph of the calibration and a label with straight line formula y = a + bx. a should be -1024 and b should be 1. If they are then we have a calibration to HU.

To demonstrate the HU calibration, move the cursor around the image and observe the "value" in the IJ status bar. The value is in HU and the gray level appears in brackets.

2. Images typically only contain 256 gray levels when displayed, even though the image may contain values of any number (eg CT from -1024 to ~32k). So gray levels have to be "binned" in an image, just like in a histogram. So the column labelled "level" is the gray level displayed in the image and the "bins" are demonstrated in the second column. The size of the bin is dictated by the min and max pixel levels.

I hope I pitched that at the right level. Enjoy ImageJ ;-)
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