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Technologies currently used for cotton contaminant assessment suffer from some fundamental limitations. These limitations result in the misassessment of the cotton quality, and have a serious impact on its economic value. Through our research, we have shown that X-ray microtomographic image analysis may be applied with a high degree of success to noninvasive evaluation of cotton for the recognition of contaminants. We believe that this procedure, when realized in real time, will have a serious impact on the cotton cleaning process, and indeed on the economic value of cotton.