UK Zebrafish Imaging and Screening Facility

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

Ventral and dorsal colour scan

Automated chemical and genetic in vivo screening of zebrafish

The Centre for Discovery Brain Sciences at the University of Edinburgh hosts the UK Zebrafish Imaging and Screening facility.

At the centre of the facility 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.

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.
  • Multiphoton holographic patterning movable objective microscope with inverted spinning disk confocal provides photomanipulation and optogenetics combined with fast gentle timelapse in vivo 3D volume imaging.
  • Two widefield automated fluorescence timelapse systems with photomanipulation and optogenetics.
  • An Apotome structured illumination system for fast widefield fixed-sample imaging
  • Behavioral imaging rigs for individual- or population-level quantification
  • A range of fluorescence compound and stereomicroscopes for routine imaging

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.

Collaborative network outlook

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




Dr Daniel Soong

Research Imaging Specialist &

UK Zebrafish Imaging and Screening Facility Manager

Centre for Discovery Brain Science

Chancellor's Building, Room GU428a,

University of Edinburgh,

49 Little France Crescent,


EH16 4SB,


Tel: 0131 242 6225