Embodiments described herein relate to an apparatus for positioning and securing an excised biological tissue specimen for imaging and analysis. In some embodiments, an apparatus includes a sample bag defining an inner volume configured to receive a biological tissue sample, and a sealing member coupled to the sample bag. An imaging window is disposed and configured to be placed in contact with at least a portion of the biological tissue sample, and a positioning member is coupled to the imaging window and is configured to be disposed against the sealing member to substantially seal the inner volume. The positioning member includes a vacuum port disposed and configured to be aligned with a vacuum source to withdraw air from the inner volume of the sample bag.