Abstract
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.
Highlights
Small size, optical transparency and ease of breeding are a few of the properties that makes the zebrafish (Danio rerio) such a desirable model organism to use for large-scale genetic or chemical screens
We have developed a two-step pipeline for correcting the errors during rotation; a global centerof-rotation correction method followed by an iterative reconstruction and registration approach with a pairwise correction strategy (Fig. 3(B))
We presented a design of a cost-effective brightfield Optical projection tomography (OPT) setup capable of rapid loading and unloading of zebrafish samples in water or glycerol
Summary
Optical transparency and ease of breeding are a few of the properties that makes the zebrafish (Danio rerio) such a desirable model organism to use for large-scale genetic or chemical screens. Using a brightfield stain, such as chromogenic in situ or Alcian blue, provides good contrast using only white transmission light. These staining techniques are less sensitive, and photobleaching and quenching are not a concern when using brightfield stains. These staining techniques are well-established, inexpensive and commonly used in zebrafish research. The biological variation between fish requires large scale experiments which is usually time consuming and requires fast sample handling and imaging
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