zOPT: an open source optical projection tomography system and methods for rapid 3D zebrafish imaging.

Zhang H, Waldmann L, Manuel R, Boije H, Haitina T, Allalou A

Biomed. Opt. Express 11 (8) 4290-4305 [2020-08-01; online 2020-07-15]

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.

BioImage Informatics [Technology development]

Bioinformatics Support for Computational Resources [Service]

Genome Engineering Zebrafish [Service]

PubMed 32923043

DOI 10.1364/BOE.393519

Crossref 10.1364/BOE.393519

pii: 393519
pmc: PMC7449731

Publications 9.5.0