VAST Imagers

VAST BioImager Platform

Automating Manipulation of Larvae for Imaging Screens

Union Biometrica develops tools for model organism research. The VAST BioImager™ platform (Vertebrate Automated Screening Technology) is designed for zebrafish researchers who need to image large numbers of 2–7 day old sedated zebrafish larvae.

Fig. 1:  Base VAST BioImager System. Inset: close-up of capillary detail.Fig. 1: Base VAST BioImager System. Inset: close-up of capillary detail.

Based on technology from the MIT (Cambridge, MA)1,2,3, VAST BioImager accelerates even the most demanding zebrafish handling and cellular-resolution imaging tasks for high-content screens. By automating the handling of larvae prior to imaging, VAST avoids the time consuming and tedious steps of manual manipulation of each larva during large screens.

Base System for Whole Zebrafish Organ-level Imaging

At the heart of VAST is a capillary where larvae can be loaded and manipulated for imaging. Batches of larvae can be loaded into the system using the 50 ml stirred conical tube sample cup. (For delivering larvae from a multi-well plate please see the autosampler option below.) Software loads larva one at a time into the capillary and positions it laterally in the field of view of the on-board high resolution camera.

VAST custom orientation

Fig. 2: Operator can select the desired orientation: lateral, dorsal or any other custom orientation.

Next the system rotates each larva 360 degrees to determine the orientation of the fish. The operator can then select the desired orientation: lateral, dorsal or any other custom orientation for image capture. All the remaining larvae will be rotated automatically to the same orientation using pattern recognition algorithms.

Once the image is captured, the software can direct the VAST unit to eject the larva to waste or dispense it to a chosen receptacle for further procedures. The VAST software allows manual or automated control of all the steps needed to capture and store images of the larvae.

Higher Resolution and Fluorescence Imaging With a Microscope

VAST BioImager

Fig. 3: VAST BioImager is a modular and expandable platform. It can be mounted on many microscopes for high resolution and fluorescence imaging.

For higher resolution imaging including cellular level imaging tasks for high content screens, VAST can be mounted on many models of upright compound microscopes or stereomicroscopes using the optional High Resolution Microscope Stage and Mounting Kit. Please see our specification sheet for critical microscope dimensions. (Note: Inverted microscopes can NOT be used.) The stage in this optional kit replaces the original stage found on select upright microscopes and enables automated micron-level positioning laterally along the zebrafish.

VAST BioImager

When using VAST with a microscope, once the larva is positioned using the on-board camera, the VAST internal light source is turned off and high-resolution images can be captured with the microscope’s optics and camera. Mounting VAST on a microscope equipped with fluorescence capability allows collection of fluorescence images.

The optional External Communications Package includes TTL inputs & outputs for automating communications with most microscopes and cameras.

Sample Introduction Options

There are 3 options for introducing larvae to the VAST system:

  • Bulk sample reservoir – via the on-board stirred 50 ml conical tube sample cup (described above)
  • From multiwell plates – via the LP Sampler
  • Individually – via the hand-held flow-through Pipettor

Optional Large Particle Sampler


Fig. 4: Optional Large Particle Sampler can gently aspirate larvae from multi-well plates.

The optional LP Sampler can be added to the system to gently aspirate larvae from multi-well plates and deliver them one at a time to VAST for imaging. This allows for increased throughput of high content assays and screens.

LP Sampler Dispenser Kit for VAST (LPS-D) turns the LP Sampler into an instrument capable of both gently aspirating and dispensing 2-7 dpf zebrafish larvae. After imaging is complete, this dispensing feature allows each larvae to be deposited into the corresponding well of a daughter plate.  This dispensing feature can also work with the VAST sample cup or the VAST Pipettor for bulk filling of multiwell plates.

Handheld Dispensing Option – A dispenser option is now available for the LP Sampler which allows you to deposit each larvae into the corresponding well of a daughter plate after imaging.  (For details please see “LP Sampler with Dispenser.pdf

Hand-held flow-through pipettor loads zebrafish to the VAST ...

Fig. 5: Hand-held flow-through pipettor loads zebrafish to the VAST one at a time at the click of a button thereby allowing the operator to “hand select” larvae.

The VAST BioImager System is a modular & expandable platform that allows researchers to avoid the tedious manual steps of loading, positioning and rotating zebrafish larvae for high-content imaging screens.


  1. Nature Methods, 2010, 7 600-601 and 634-636, Carlos Pardo-Martin, Tsung-Yao Chang, Bryan Kyo Koo, Cody L Gilleland, Steven C Wasserman and Mehmet Fatih Yanik
  2. Lab Chip, 2012, 12 711-716, Tsung-Yao Chang, Carlos Pardo-Martin, Amin Allalou, Carolina Wählby and Mehmet Fatih Yanik
  3. Nature Communications, 4, Article number:1467, doi:10.1038/ncomms2475, Carlos Pardo-Martin, Amin Allalou, Jaime Medina, Peter M. Eimon, Carolina Wählby, Mehmet Fatih Yanik

VASTomography™ Software Enables 3D Zebrafish Research

  • Ability to generate 3D optical projection tomography (OPT) in minutes
  • Data sets of volume, shape and position for selected region of interest
  • 3D visualization with VolView/ParaView
  • Data processing with MATLAB/Python

VAST Tomography

Figure. 6: Constructing tomography from fluorescent images of 4 dpf zebrafish larvae labeled with Col2-H2a-mCherry. A) Ventral view. B) Lateral view. C) 3D tomography of the same fish by VASTomography software.

Optical projection tomographic reconstruction (OPT) builds a 3D density model of the zebrafish larva based on light transmission through the sample. VASTomographyTM is a software tool that transforms rotational image data collected by the VAST camera or microscope cameras to a format that can be visualized and processed in 3D. The reconstructed tomography file can be visualized in open source software such as VolView or ParaView. The tomography matrix data can also be processed using MATLAB or Python. Additionally, the ‘alpha shape’ feature in the software calculates volume and surface area of selected region of interest. Positional, volumetric and shape information can now be readily visualized and collected for further investigation. (See QTN-026 for more details.)


The VAST BioImager System is a modular & expandable platform that allows researchers to avoid the tedious manual steps of loading, positioning and rotating zebrafish larvae for high-content imaging screens.


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