Edinburgh’s main brain-imaging facility is running at near-total capacity, with each of its confocal microscopes averaging 1,320 hours of use per year out of a possible 1,400. To keep up with demand from over 300 scientists, the team wants to buy a new spinning disk microscope that will cut imaging time tenfold without losing resolution. The current point-scanning machines force a trade-off between image size and speed when mapping whole brain slices, organoids, and other large samples. The new system will also add automated, AI-driven imaging and analysis, and allow simultaneous dual-colour recording of fast events such as calcium signalling and voltage sensing in living cells. Crucially, the microscope’s super-resolution mode will let researchers see subcellular details within the context of whole tissues, bridging scales that are now hard to link. If successful, the upgrade will let Edinburgh develop spatial transcriptomics pipelines—techniques that map neural connections alongside gene expression—currently available in only a handful of US labs. This is fundamental science aimed at understanding neurodevelopment and organ formation; it does not have an immediate clinical application, but similar imaging advances have historically opened unexpected routes into disease mechanisms and drug discovery.
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The IMPACT imaging facility delivers microscope imaging capability for over 300 scientists, students and support staff within the Centre for Discovery Brain Sciences (CDBS), Institute of Neuroscience and Cardiovascular Research (INCR), University of Edinburgh (UoE). As part of the Edinburgh Bio-Imaging Consortium we also offer our services across the whole UoE and to external academic and commercial clients. Our confocal microscopes are currently being used at near 100% of capacity (where 100% capacity is considered to be 1400 hours per year), each averaging 1320 hours of use per year. Here we are seeking funding to purchase the next generation of spinning disk confocal microscope to increase the capacity that the facility can offer and maximise throughput. The microscope we have chosen will also bring automated, AI-driven imaging and analysis capabilities to the facility. The facility’s users routinely image whole brain and organ slices from a variety of model organisms, as well as intact organoids, to increase our basic understanding of neurodevelopment, neurophysiology and organogenesis. For imaging of large areas our point-scanning confocal microscopes force a trade-off between resolution and total time required for acquisition. We wish to purchase the Nikon Crest-Optics X-LightV3/DeepSIM spinning disk microscope which produces the largest images, with the flattest illumination field currently available, utilising the full 25mm field of view in the optical light path. The incorporation of two Photometrics Kinetix sCMOS cameras will allow simultaneous dual-colour imaging, enhancing the speed of acquisition of fixed tissue images. This new imaging technology will reduce our imaging time by 10-fold compared to our point scanning confocals with no sacrifice in resolution. Furthermore, this new technology will allow UoE to develop spatial transcriptomics pipelines, integrating projectome mapping (the network of neural connections) with transcriptome profiling (gene expression data), advanced techniques currently restricted to a few labs exclusively in the United States. Spinning disk microscopes are well regarded for minimising phototoxicity while imaging live cells and tissues. The combination of spinning disk technologies with the fast imaging rates of Kinetix cameras (>1000fps) will allow the simultaneous recording of integrated, highly dynamic events, such as image based voltage sensing and calcium signalling, within cells and tissues. The Crest-Optics DeepSIM super-resolution modality, combined with the spinning disk, will create an imaging system capable of imaging across scales, contextualising subcellular events within a tissue. The hardware control is fully integrated within NIS-Elements. Combining the hardware with the AI image processing features available within Nikons-Elements, and the JOBS graphical programming package, will allow automatic imaging protocols to be developed to identify and image rare or event-driven instances with fixed or live tissue. The system will be housed in a dedicated imaging facility managed by two full time members of staff who are imaging and image analysis specialists. The facility business plan allows us to keep all of our instruments under fully inclusive service and repair packages, minimising uncertainty of downtime of any of our systems. The IMPACT facility is part of the Edinburgh Bio-Imaging Consortium which brings together over 30 bio-imaging and analysis experts from across Edinburgh and Heriot-Watt Universities. We use this critical mass of expertise to provide an all-encompassing support network for our users, sharing equipment and resources, and collectively negotiating best-value for procurement.
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