A method for processing input image voxel data representative of 3-dimensional images of a colon having gas and stool tagged with stool tagging agent and generated by an imaging instrument having a point spread function, to remove the stool from the images, characterised by the following steps: a. classifying the voxels into one of a plurality of class masks including tagged stool, gas, tissue and unknown substance masks as a function of the intensities and gradients of the voxels; b. attempting to reclassify at least some of the voxels in the unknown substance mask into one or more of the tagged stool, gas and tissue masks as a function of the classification of adjacent voxels; c. after step b, attempting to reclassify at least some of the voxels in the unknown substance mask into the tagged stool mask if the voxels in the unknown substance mask are surrounded by voxels in the tagged stool mask; d. after step c, attempting to reclassify at least some of the voxels in the unknown substance mask into the tagged stool mask as a function of the intensities of the voxels in the unknown substance mask; e. after step d, repeating step b; f. after step e, repeating step c; g. after step f, dilating the tagged stool, gas and tissue masks as a function of the point spread function of the instrument; h. after step g, reclassifying voxels of the tagged stool mask that overlap with voxels in the tissue mask into the tissue mask; i. after step h, convolving voxels in the tagged stool mask with the point spread function of the instrument to generate an estimate of the fractional contribution of stool to the intensity at voxels in the input image voxel data; and j. reducing the intensities of voxels in the input image voxel data as a function of the stool amount estimates generated in step i. a. classifying the voxels into one of a plurality of class masks including tagged stool, gas, tissue and unknown substance masks as a function of the intensities and gradients of the voxels; b. attempting to reclassify at least some of the voxels in the unknown substance mask into one or more of the tagged stool, gas and tissue masks as a function of the classification of adjacent voxels; c. after step b, attempting to reclassify at least some of the voxels in the unknown substance mask into the tagged stool mask if the voxels in the unknown substance mask are surrounded by voxels in the tagged stool mask; d. after step c, attempting to reclassify at least some of the voxels in the unknown substance mask into the tagged stool mask as a function of the intensities of the voxels in the unknown substance mask; e. after step d, repeating step b; f. after step e, repeating step c; g. after step f, dilating the tagged stool, gas and tissue masks as a function of the point spread function of the instrument; h. after step g, reclassifying voxels of the tagged stool mask that overlap with voxels in the tissue mask into the tissue mask; i. after step h, convolving voxels in the tagged stool mask with the point spread function of the instrument to generate an estimate of the fractional contribution of stool to the intensity at voxels in the input image voxel data; and j. reducing the intensities of voxels in the input image voxel data as a function of the stool amount estimates generated in step i.