Optical Projection Tomography for Particle Counting and Morphology Analysis Olli Koskela 1,2(B ) , Md Tanvirul Kabir Chowdhury 1 , Toni Montonen 1 , Birhanu Belay 1 , Sampsa Pursiainen 3 , and Jari Hyttinen 1 1 Faculty of Medicine and Health Technology and BioMediTech Institute, Tampere University, Tampere 33014, Finland olli.koskela@hamk.fi 2 HAMK Smart Research Unit, H¨ame University of Applied Sciences, H¨ ameenlinna, Finland 3 Faculty of Information Technology and Communication Sciences, Tampere University, Tampere 33014, Finland Abstract. Optical projection tomography (OPT) is a powerful tech- nique for imaging in developmental biology. It is similar to X-ray com- puted tomography where shadowgrams of rays transmitted through sam- ple 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, con- sequently, 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 reconstruc- tion 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. Keywords: Optical projection tomography · Microscopy · Fluorescence microscopy · Brightfield microscopy 1 Introduction Optical projection tomography (OPT) is an imaging technique similar to X- ray computed tomography (CT), except that in OPT light is projected through transparent sample instead of X-rays [1]. Hence OPT has in many cases practi- cally negligible effect on living cells, thus enabling long term imaging of living c  Springer Nature Switzerland AG 2021 T. Jarm et al. (Eds.): EMBEC 2020, IFMBE Proceedings 80, pp. 944–951, 2021. https://doi.org/10.1007/978-3-030-64610-3_105