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zOPT: an open sourc...
zOPT: an open source optical projection tomography system and methods for rapid 3D zebrafish imaging
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- Zhang, Hanqing (författare)
- Uppsala universitet,Bildanalys och människa-datorinteraktion,Science for Life Laboratory, SciLifeLab,Avdelningen för visuell information och interaktion
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- Waldmann, Laura (författare)
- Uppsala universitet,Evolution och utvecklingsbiologi
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- Manuel, Remy (författare)
- Uppsala universitet,Boije: Zebrafiskens neuronala nätverk
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- Boije, Henrik (författare)
- Uppsala universitet,Boije: Zebrafiskens neuronala nätverk
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- Haitina, Tatjana, Docent, 1981- (författare)
- Uppsala universitet,Evolution och utvecklingsbiologi
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- Allalou, Amin, 1981- (författare)
- Uppsala universitet,Science for Life Laboratory, SciLifeLab,Bildanalys och människa-datorinteraktion
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(creator_code:org_t)
- The Optical Society, 2020
- 2020
- Engelska.
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Ingår i: Biomedical Optics Express. - : The Optical Society. - 2156-7085. ; 11:8, s. 4290-4305
- Relaterad länk:
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https://doi.org/10.1...
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https://uu.diva-port... (primary) (Raw object)
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https://urn.kb.se/re...
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https://doi.org/10.1...
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Abstract
Ämnesord
Stäng
- 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.
Ämnesord
- TEKNIK OCH TEKNOLOGIER -- Medicinteknik -- Medicinsk bildbehandling (hsv//swe)
- ENGINEERING AND TECHNOLOGY -- Medical Engineering -- Medical Image Processing (hsv//eng)
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- art (ämneskategori)
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