Silhouette-based 3D model for zebrafish high-throughput imaging

Guo, Yuanhao; Veneman, Wouter J.; Spaink, Herman P.; Verbeek, Fons J.

doi:10.1109/ipta.2015.7367175

Cited by 6 publications

(3 citation statements)

References 24 publications

(29 reference statements)

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“…Brightfield images, on the other hand, will give all information on shape and size if they present an overview of the specimen. Therefore, we investigate how the axial-view images can be employed to obtain precise and accurate measurements on size and shape [3]. We will use the VAST-system to produce a full revolution of the specimen and acquire, with the VAST-camera, a set of axialview images.…”

Section: Reservoir For Zebrafishmentioning

confidence: 99%

See 1 more Smart Citation

Three-dimensional reconstruction and measurements of zebrafish larvae from high-throughput axial-view in vivo imaging

Guo¹,

Veneman²,

Spaink³

et al. 2017

Biomed. Opt. Express

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High-throughput imaging is applied to provide observations for accurate statements on phenomena in biology and this has been successfully applied in the domain of cells, i.e. cytomics. In the domain of whole organisms, we need to take the hurdles to ensure that the imaging can be accomplished with a sufficient throughput and reproducibility. For vertebrate biology, zebrafish is a popular model system for high-throughput applications. The development of the Vertebrate Automated Screening Technology (VAST BioImager), a microscope mounted system, enables the application of zebrafish high-throughput screening. The VAST BioImager contains a capillary that holds a zebrafish for imaging. Through the rotation of the capillary, multiple axial-views of a specimen can be acquired. For the VAST BioImager, fluorescence and/or confocal microscopes are used. Quantitation of a specific signal as derived from a label in one fluorescent channel requires insight in the zebrafish volume to be able to normalize quantitation to volume units. However, from the setup of the VAST BioImager, a specimen volume cannot be straightforwardly derived. We present a high-throughput axial-view imaging architecture based on the VAST BioImager. We propose profile-based 3D reconstruction to produce 3D volumetric representations for zebrafish larvae using the axial-views. Volume and surface area can then be derived from the 3D reconstruction to obtain the shape characteristics in high-throughput measurements. In addition, we develop a calibration and a validation of our methodology. From our measurements we show that with a limited amount of views, accurate measurements of volume and surface area for zebrafish larvae can be obtained. We have applied the proposed method on a range of developmental stages in zebrafish and produced metrical references for the volume and surface area for each stage.

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Section: Reservoir For Zebrafishmentioning

confidence: 99%

“…the VAST-camera. Therefore we have proposed [3] a method similar to ideas on texture registration and stitching [20]. We define the area coherence as the area of overlap between the image projected from the 3D reconstructed model and the groundtruth profile.…”

Section: Camera System Optimizationmentioning

confidence: 99%

Three-dimensional reconstruction and measurements of zebrafish larvae from high-throughput axial-view in vivo imaging

Guo¹,

Veneman²,

Spaink³

et al. 2017

Biomed. Opt. Express

Self Cite

View full text Add to dashboard Cite

show abstract

“…One can also estimate an enclosed 3D surface from the voxels. For more details of the profile-based 3D reconstruction, we refer to our previous work [12,18]. The green line denotes the profile-axis along which the object revolves.…”

Section: Profile-based 3d Reconstructionmentioning

confidence: 99%