UK Zebrafish Imaging and Screening Facility

Functional imaging and automated chemical and genetic in vivo screening of zebrafish

Dr. Daniel Soong

Research Imaging Specialist & UK Zebrafish Imaging and Screening Facility Manager

Institute for Neuroscience and Cardiovascular Research,

Chancellor's Building, Room GU428a,

University of Edinburgh,

49 Little France Crescent,

Edinburgh, EH16 4SB

Contact details

Email: daniel.soong@ed.ac.uk

Tel: (0)+44 131 242 6225

Automated chemical and genetic in vivo screening of zebrafish

The Centre for Discovery Brain Sciences, within the Institute for Neuroscience and Cardiovascular Research at the University of Edinburgh, hosts the UK Zebrafish Imaging and Screening Facility.

At the centre of the facility’s screening capability is an automated zebrafish embryo handling system (VAST, Union Biometrica), which combined with a high-speed spinning disk confocal microscope (Zeiss/Yokogawa) allows for rapid screening of entire larvae in 3D confocal stacks.

We specialise in automated multiscale acquisition and AI-based automated analysis of images of all modalities, minimising manual analysis, maximising quantifiable and reproducible results, and freeing up researcher time to focus on the bigger picture.

Our range of microscopes are designed to capture whole organisms with minimal invasiveness or interference, at multiple scales, using both detailed structural images and high speed functional images. Many of our systems are geared towards application of optomanipulation as part of the imaging parameters or experimental design.

Specialist functional and structural imaging

The facility supplies access to, training on, and imaging assistance with a range of advanced light microscopes focused on recording fast functional processes in vivo as well as a host of modalities for structural imaging, screening, and routine microscopy.

LSM880 confocal with Airyscan, allowing for fast super resolution confocal imaging of dynamic processes in vivo as well as high quality multichannel super resolution structural 3D volumes.
MP-NSPARC confocal-multiphoton-super resolution hybrid system for fully automated AI-driven imaging of multiple whole live zebrafish at multiple scales simultaneously. This system is designed to achieve structural and functional imaging, with optogenetic stimulation or ablation, from whole organism to single-cell super resolution, across multiple anatomical and biological systems at once, in tens of larvae, during a single automated run.
Two widefield automated fluorescence timelapse systems with photomanipulation and optogenetics.
An Apotome structured illumination system for fast widefield fixed-sample imaging
Behavioural imaging rigs for individual- or population-level quantification
A range of fluorescence compound and stereomicroscopes for routine imaging and sample preparation.

Automated quantitative image analysis

All imaging in the facility is geared towards acquisition of quantifiable data. As such, the facility provides training in a range of image analysis tools and packages and, upon request, can engage in direct project assistance for experimental design, custom image analysis scripts, machine learning, and automated analysis pipelines.

We run image analysis as a service or through collaboration.

Collaborative network outlook

The UK Zebrafish Imaging and Screening Facility is open to academic or industry collaborators from the UK and internationally.