Confocal and Advanced Light Microscopy (CALM) Facility - Edinburgh

The CALM Facility provides open-access, imaging-related services to researchers at the University of Edinburgh and beyond. As well as offering basic light microscopy services (experimental design, wide-field and confocal microscopy, image analysis and consultancy) the CALM Facility has specialised in live specimen imaging involving the most common animal models. As such, we provide the infrastructure, expertise and equipment for advanced, intravital, multi-dimensional optical imaging.


Imaging Platforms

Keywords - Light Microscopy: Confocal microscopy | Widefield microscopy | Laser microdissection | Live cell imaging | Multi-photon microscopy | TCSPC-FLIM | Light-sheet microscopy (SPIM) | Raman imaging 

Andor spinning disk confocal microscope with 5 lasers, laser-based micromanipulation unit, fully controlled enclosure, fast emission filter wheel, variable beam splitter and 2 EMCCD cameras
LaVision Biotec customised laser scanning system for MP excitation and deep penetration imaging. The system is laid out for high-content, multi-mode intravital imaging. It includes two Coherent Ultra II lasers, Coherent OPO, upright intravital stage, inverted stand with large motorised table, galvo and resonant scanner, standard PMT, GaAsP and TCSPC detectors, adaptive optics, visible laser for photo-activation and a range of high NA, water-corrected lenses. The system can record up to 6 fluorescent channels and vibrational signals (SHG, THG, CARS), fully enclosed and temperature-controlled.
Custom-built SPIM for 3 spectral channels
Inverted Leica SP5 TCS with 3 spectral channels
Leica TCS SP8
Range of upright and inverted wide-field fluorescence microscopes


Keywords - Biological: Cell Biology | Neurobiology | Developmental Biology | Zebrafish | Physiology

The CALM Facility offers support for the experimental design and practical delivery of live- and fixed-specimen imaging experiments, including the processing of a wide range of specimens and samples (please enquire). Some of the advanced applied imaging technologies are: longitudinal studies, TCSPC-based fluorescence lifetime measurements, wave front modulation by adaptive optics, deep optical sample penetration, photo-manipulation (activation, conversion, ablation, etc), fast multi-dimensional image acquisition.

Sample Preparation

Keywords - Biological: Resin embedding | Serial sectioning | Cryosectioning | Plunge Freezing | Freeze substitution | Photoconversion | Immunofluorescence | H&E staining | Live Cell | Live specimens

The CALM Facility provides support for the planning and practical preparation of a wide range of live specimen imaging experiments. The facility is part of the service umbrella SuRF@QMRI (Shared University Research Facilities) and we are working very closely with the Histology and Immuno-detection unit of SuRF. This unit provides a large range of services for sample fixation and sectioning (cryo and embedded tissues). The services on offer include fully automated histo-immuno labelling and fluorescence-based immuno-detection. This unit also operates two Zeiss Axioscan.Z1 slide scanners for high throughput image acquisition (fluorescence and brightfield image acquisition). 

Data Analysis

Keywords - Software: ImageJ | FIJI | Imaris | Matlab | Huygens | Volocity | AxioVision | ImSpectorPro

A range of workstations is available for using the following image analysis packages: ImageJ/Fiji, MatLab, Volocity, Huygens and Imaris. The CALM Facility provides training and support for this image analysis infrastructure. Users also have access to the ‘Eddie’ large Linux Compute Cluster operated by the Edinburgh Compute and Data Facility for high performance computing. This includes an Omero installation for handling and archiving of image data.

Shared Access

The CALM Facility is operated as an open-access unit, providing imaging services to the biomedical research community at the University of Edinburgh. Academic and commercial projects from outside the University are welcome and can be discussed.


The CALM facility is funded by the College for Medicine and Veterinary Medicine (University of Edinburgh) and the Research Councils UK. The operation and maintenance of the facility is funded by usage charges.

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