zOPT: an open source optical projection tomography system and methods for rapid 3D zebrafish imaging.
| Autor: | Zhang H; Division of Visual Information and Interaction, Department of Information Technology, Uppsala University, S-75105 Uppsala, Sweden.; BioImage Informatics Facility at SciLifeLab, S-75105 Uppsala, Sweden., Waldmann L; Department of Organismal Biology, Uppsala University, S-75236 Uppsala, Sweden., Manuel R; Department of Neuroscience, Uppsala University, S-75124 Uppsala, Sweden., Boije H; Department of Neuroscience, Uppsala University, S-75124 Uppsala, Sweden., Haitina T; Department of Organismal Biology, Uppsala University, S-75236 Uppsala, Sweden., Allalou A; Division of Visual Information and Interaction, Department of Information Technology, Uppsala University, S-75105 Uppsala, Sweden.; BioImage Informatics Facility at SciLifeLab, S-75105 Uppsala, Sweden. |
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| Jazyk: | angličtina |
| Zdroj: | Biomedical optics express [Biomed Opt Express] 2020 Jul 15; Vol. 11 (8), pp. 4290-4305. Date of Electronic Publication: 2020 Jul 15 (Print Publication: 2020). |
| DOI: | 10.1364/BOE.393519 |
| Abstrakt: | Optical projection tomography (OPT) is a 3D imaging alternative to conventional microscopy which allows imaging of millimeter-sized object with isotropic micrometer resolution. The zebrafish is an established model organism and an important tool used in genetic and chemical screening. The size and optical transparency of the embryo and larva makes them well suited for imaging using OPT. Here, we present an open-source implementation of an OPT platform, built around a customized sample stage, 3D-printed parts and open source algorithms optimized for the system. We developed a versatile automated workflow including a two-step image processing approach for correcting the center of rotation and generating accurate 3D reconstructions. Our results demonstrate high-quality 3D reconstruction using synthetic data as well as real data of live and fixed zebrafish. The presented 3D-printable OPT platform represents a fully open design, low-cost and rapid loading and unloading of samples. Our system offers the opportunity for researchers with different backgrounds to setup and run OPT for large scale experiments, particularly in studies using zebrafish larvae as their key model organism. Competing Interests: The authors declare no conflicts of interest. (© 2020 Optical Society of America under the terms of the OSA Open Access Publishing Agreement.) |
| Databáze: | MEDLINE |
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