Light Microscopy

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Overview

The Light Microscopy Facility specialises in basic and advanced fluorescence microscopy techniques. Microscopy is the gold standard technique for the morphological analysis of cells and tissues. We provide researchers with access to advanced imaging instruments, technical expertise, and training. Its purpose is to enable high-quality, reproducible imaging for a wide range of biological and materials science applications. Refer to the equipment summary dropdown to discover the capabilities of our microscopes.

The facility provides:

Advice on selecting the right microscope and imaging modalities
In-depth training for autonomous instrument operation
Guidance on experimental design, sample preparation, image acquisition, and optimization
Assistance with complex or cutting-edge imaging techniques
Help with troubleshooting and data interpretation
Workstations and software for quantitative image analysis (e.g., FIJI/ImageJ, Huygens)
Support with segmentation, tracking, colocalization, 3D reconstruction, machine-learning–based analysis
Data storage solutions and workflow guidance for large imaging datasets

Our overall mission is to enable high-quality, cutting-edge imaging by:

Making expensive instruments accessible to many researchers
Ensuring proper training and reproducibility
Providing expert guidance to maximize scientific impact

Light Microscopy Core Facility Equipment

Equipment Summary

Table 1. Microscope types in the Core Facility.

Table 1. Microscope type. *System is upright, not a typical live cell set-up.
	Nikon Eclipse E600	Olympus IX81	Olympus FV1000	Olympus FV3000	Leica Stellaris Dive Falcon	Zeiss Elyra7 Lattice SIM
Inverted/Upright	Upright	Inverted	Inverted	Inverted	Upright	Inverted
Widefield Epifluorescence	Yes	Yes	-	-	-	Yes
Brightfield	Yes	Yes	Yes	Yes	Yes	Yes
Darkfield	Yes	-	-	-	-	-
Differential Interference Contrast (DIC)	-	-	-	Yes	-	Yes
Laser Scanning Confocal	-	-	Yes	Yes	Yes	-
Multiphoton	-	-	-	-	Yes	-
Fluorescence Lifetime Imaging (FLIM)	-	-	-	-	Yes	-
Structured Illumination Microscopy (SIM)	-	-	-	-	-	Yes
Super Resolution	-	-	-	-	-	Yes

Table 2. Experiment / Sample types each microscope can work with. *System is upright, not a typical live cell setup.

Table 2. Experiment and sample types. *System is upright, not a typical live cell set-up
	Nikon Eclipse E600	Olympus IX81	Olympus FV1000	Olympus FV3000	Leica Stellaris Dive Falcon	Zeiss Elyra7 Lattice SIM
Timelapse imaging with temperature, O2 and CO2 control	-	-	-	Yes	Yes*	Yes
Fast timelapse imaging	-	-	-	-	-	Yes
Fixed/unfixed cells/spheroids in multi-well dishes	-	Yes	Yes	Yes	-	Yes
Fixed cells on slides	Yes	Yes	Yes	Yes	Yes	Yes
Small spheroids/organoids	-	-	Yes	Yes	Yes	-
Large spheroids/organoids	-	-	-	-	Yes	-
Thin tissue sections	-	-	Yes	Yes	Yes	Yes
Thick tissue sections	-	-	Yes	Yes	Yes	-
Large gels with cells/spheroids or cleared tissue	-	-	-	-	Yes	-

For a more comprehensive breakdown of each microscope, click on the equipment names below.

Zeiss Elyra 7 Lattice SIM

Type / technique: Inverted super-resolution structured illumination microscope

The Zeiss Elyra 7 microscope achieves super resolution from the structured Illumination process along with computer processing and deconvolution. This is a fast, camera-based system, and can be used for both fixed and live samples, and is compatible with multiwell dishes.
Super resolution imaging is achieved using the 63x oil lens. Here a lattice blocks out some of the illumination light, the lattice is rotated and multiple images of the same field of view are acquired. The images acquired when the lattice was in different phases are used to reconstruct a super-resolution image. The SIM2 algorithm may also be applied to further increase resolution using deconvolution. Outside of super resolution the system can also be used to generate confocal-like images with optical sectioning using the Apotome mode. Here a striped grid blocks out some of the illumination light, like above, images are acquired with the grid in different phases. These images are then processed to better resolve structures of interest.

Microscope base: Axio Observer 7 inverted
Lightsource: 405, 488, 561 and 642 nm lasers
Detection: 2 Hamamatsu ORCA-fusion BT cameras
Objective lenses: 2.5X, 10X, 25X (multi-immersion), 40X (oil), 40X (water), 63X (oil), 63X (water)
Transmitted light: brightfield, DIC (using 10X or 63X water)
XYZ control: Motorized XYZ control
Incubation temp and CO2 control: yes
Optical sectionins: yes, structured illumination lattice or apotome mode
Software: ZenBlue

Leica Stellaris Dive Falcon

Type / technique: Confocal, multiphoton, fluorescence lifetime imaging.

The Leica Stellaris Dive is a microscope with dual functionality. It is in an upright configuration and can be used for regular laser scanning confocal microscopy as well as multiphoton microscopy. The change from confocal to multiphoton mode is seamless and completed by the STO, it consists of activating the multiphoton lasers and changing the nosepiece of the microscope so that it houses the 25X multiphoton water dipping lens. As a confocal microscope, due to its upright configuration it is most suitable for fixed samples which are mounted with a coverslip rather than samples in multiwell dishes. If the samples are three dimensional, they can be mounted with silicone spacers and imaged using confocal or multiphoton mode.

Where the system really shines is in multiphoton mode. Samples like spheroids encased in gels are imaged in petri dishes in an aqueous solution such as PBS, the multiphoton lens dips directly into this solution. The system is designed for deep cell/tissue imaging, the multiphoton lens has a long working distance and the theoretical z limit for imaging is in the mm range, although the actual results will depend on the density of the sample and depth of penetration of the fluorophores. The system in multiphoton mode can also be used to image thick mounted and cleared samples of tissue by simply placing a large drop of water on-top of the coverslip. The system is also equipped with FAst Lifetime CONtrast (FALCON) module for FLIM experiments. FLIM is a technique which can be used to separate fluorescence emissions which overlap in the same channel, for example tissue autofluorescence and GFP expression. This is due to differences in the fluorescence lifetime properties molecules which auto fluoresce and dyes of interest.

Microscope base: Leica DM6 upright
XYZ control: Motorized XYZ control
Incubation temp and CO2 control: yes
Software: LAS-X

Laser Scanning Confocal

Lightsource: 405, 488, 561 and 638 nm lasers
Detection: Tuneable emission using HyD S 1, HyD S 2, HyD S 3, HyD X 4 detectors
Scanner: Galvo (standard) or resonant (fast)
Objective lenses: 10x, 20x (multi-immersion), 40x (glycerol), 63x (oil).

Multiphoton

Lightsource: tuneable 680-1300nm and a 1045nm femtosecond pulsed lasers (Insight dual IR)
Objective lens: 25x long working distance water dipping lens with motorised correction collar
Detection: Tuneable emission using 3 non-descanned detectors located withing Deep In-Vivo Explorer (DIVE) module

Olympus FV3000

Type: Inverted laser scanning confocal microscope

The Olympus FV3000 is an inverted laser scanning confocal microscope which is perfect for imaging both live or fixed biological samples. The system is equipped with DIC and allows for simultaneous imaging using DIC and fluorescence channels. It is equipped with an incubation chamber and CO2/O2 control and so is suitable for time-lapse imaging. The system also has a resonant scanner which can be used for fast live cell imaging. The emission is detected using 4 detectors allowing for simultaneous imaging of four spectrally separated channels, while the detectors themselves can be tuned to specific emission ranges. This system was installed back in 2018 and quickly became the workhorse of the facility due to its to its user-friendly design as well as versatility in the types of samples that it can image. This system is well suited for imaging samples in multi-well dishes, fixed slides of cells or tissues and even small spheroids/organoids.

Microscope base: Inverted Olympus IX81
Lightsource: 405, 488, 543 and 633 nm lasers
Detection: 2 high sensitivity (HSD) and 2 standard PMT detectors (SD)
Scanner: Resonant (high speed) and Galvo (standard)
Objective lenses: 2x, 4x, 10x, 20x (air or oil), 30x (silicone), 40x (air, water or silicone), 60x (oil), 100x (oil)
Transmitted light: brightfield, DIC (compatible with LSM)
Emission: Tuneable detection range down to 1nm accuracy
XYZ control: Motorized XYZ control
Incubation temp and CO2 control: yes
Software: Fluoview

Witec Alpha500

Type / technique: Raman Spectroscopy

This system is used to generate raman spectra from a wide variety of materials from inorganic to complex biomaterials and tissues. The system can scan a fixed point, 2 d maps and also scan in z. Very little sample preparation is involved, quartz is the recommended substrate for holding the samples of interest. We primarily run assisted sessions on this instrument but is available for autonomous use pending extensive training.

Microscope Base: upright frame gantry arrangement
Lightsource: XTRA high power single frequency diode 785nm laser
Optical sectioning: yes confocal
Objective lenses: 10x, 20x, 40x, 60x, 100X
XYZ control: Motorized XYZ control

Olympus IX81

Type: Inverted Widefield Fluorescence System

The Olympus IX81 is an inverted fluorescence microscope which uses a 16 colour LED light source and traditional DAPI, FITC, TRITC and Cy5 filter sets. The system is equipped with motorized z control allowing users to acquire 3D z-stacks in multiple channels. In 2022 the system the system was fitted with a modern LED light source, new camera, new PC, and opensource software MicroManager for acquisition of images.

Microscope base: Inverted Olympus IX81
Lightsource: COOLLED pE-4000, 16 colour LED source
Detection: Hamamatsu ORCA-Flash4.0L C11440 digital camera
Objective lenses: 4X, 10X, 20X, 40X (oil), 60X (oil) 100X (oil)
Epi fluorescence: DAPI, FITC, TRITC, Cy5 classic filter sets
XYZ control: Manual XY, motorized Z control
Software: MicroManager (open source)

Olympus FV1000

Type: Inverted laser scanning confocal microscope

The Olympus FV1000 is an inverted laser scanning confocal microscope which is perfect for imaging both live or fixed biological samples. The system is not equipped with an incubation chamber and so is not suitable for time-lapse imaging which requires incubation and CO2/O2 control. Although it is an older system it still functions well and is the only laser scanning confocal system located in the biomedical sciences building.

Microscope base: Inverted Olympus IX71
Lightsource: 405, 473, 546, 633nm excitation lasers
Detection: 3 tuneable PMT detectors
XYZ control: Motorized XYZ control
Software: Evident Fluoview

Nikon Eclipse

Type: Upright Widefield Fluorescence System with a Darkfield Setup

The Nikon Eclipse E600 is an upright fluorescence microscope which uses an LED light source and classical DAPI, FITC, TRITC filter sets. In 2016 the system was upgraded with a dark-field set-up while other optics and camera was upgraded in 2024.