Muscle tissue segmentation in CT images


I am starting a new project on quantifying muscle tissue in mid-abdominal CT slices. Many papers have use ImageJ with reliable measurements, but I’m having a hard time reading compressed DICOM images.

I’m using BioFormats to import the image stacks but I just can’t make it automatically go to Hounsfield Unit scale instead of that 0-255 scale. Any help is more than welcome.

report what do you use to read the images, it may happen you images are stored as 8-bit images, check that.

I actually use:

Calibration cal = imp.getCalibration();	// here we get height, width and depth of pixel.
double vw = cal.pixelWidth;			//  pixel width
double vh = cal.pixelHeight;			// pixel height
double vd = cal.pixelDepth;                   //  pixel depth
float[][] pixels = ip.getFloatArray();		// image pixel values (HU units in CT image)
int ns = imp.getStackSize();                  // number of images in the stack