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zOPT: an open sourc...
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Zhang, HanqingUppsala universitet,Bildanalys och människa-datorinteraktion,Science for Life Laboratory, SciLifeLab,Avdelningen för visuell information och interaktion
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zOPT: an open source optical projection tomography system and methods for rapid 3D zebrafish imaging
- Article/chapterEnglish2020
Publisher, publication year, extent ...
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The Optical Society,2020
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electronicrdacarrier
Numbers
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LIBRIS-ID:oai:DiVA.org:uu-419799
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https://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-419799URI
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https://doi.org/10.1364/BOE.393519DOI
Supplementary language notes
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Language:English
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Summary in:English
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Subject category:ref swepub-contenttype
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Subject category:art swepub-publicationtype
Notes
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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.
Subject headings and genre
Added entries (persons, corporate bodies, meetings, titles ...)
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Waldmann, LauraUppsala universitet,Evolution och utvecklingsbiologi(Swepub:uu)lauwa544
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Manuel, RemyUppsala universitet,Boije: Zebrafiskens neuronala nätverk(Swepub:uu)remma294
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Boije, HenrikUppsala universitet,Boije: Zebrafiskens neuronala nätverk(Swepub:uu)henbo576
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Haitina, Tatjana,Docent,1981-Uppsala universitet,Evolution och utvecklingsbiologi(Swepub:uu)tahai516
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Allalou, Amin,1981-Uppsala universitet,Science for Life Laboratory, SciLifeLab,Bildanalys och människa-datorinteraktion(Swepub:uu)amial914
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Uppsala universitetBildanalys och människa-datorinteraktion
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Related titles
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In:Biomedical Optics Express: The Optical Society11:8, s. 4290-43052156-7085
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