Optical Projection Tomography for Particle Counting and Morphology Analysis

Optical projection tomography (OPT) is a powerful technique for imaging in developmental biology. It is similar to X-ray computed tomography where shadowgrams of rays transmitted through sample are recorded and, based on these shadowgrams, the internal structure of the sample is reconstructed. In OPT however, light is used instead of X-rays, which provides practically negligible effect to the sample in many cases. OPT can also be used in fluorescent mode, where emission of the excited fluorescent markers is imaged. The optical instrumentation, consequently, imposes blurring into sample details outside the focal plane of the imaging objective. To increase the quality of the tomographic reconstructions, we incorporated light beam model into the reconstruction process, both in transmission brightfield and in fluorescent emission modes. In this work, we quantitatively compare the performance the new models with that of conventional filtered backprojection. Based on our results, the incorporated light models and filtered backprojection perform close to each other. Noise-reduction improved the quantified measures in filtered backprojection case when 400 projection angles were used. We provide the related data and codes.