BCI Light Microscopy Core Facility

Our Microscopy Facility provides a collection of light microscopes to suit a wide range of applications. This service offers support, advice and training for researchers both within and beyond the Institute.

Our equipment includes confocal, laser microdissection, timelapse, stereo and scanning systems. We have dedicated analysis workstations with access to imaging software including MetaMorph® and Imaris.

The facility recently moved to a refurbished suite of rooms. Please contact us about your imaging requirements.


Information for Users

Location: John Vane Science Centre, Charterhouse Square, London

Microscopy Facility Manager: Linda Hammond

Contact for enquiries/training: l.j.hammond@qmul.ac.uk 

Booking: Online booking system - iLab Solutions

Internal Users

Please visit the BCI Intranet


We have two laser scanning confocal microscopes in the imaging suite, each equipped with 4 lasers.

Both are inverted and fitted with an incubation chamber, allowing users to perform live imaging experiments that can be recorded as a time series.

The confocal pinhole ensures that only features in the plane of focus are collected by the detector. By imaging a number of overlapping slices throughout the specimen, the 3 dimensional structure of a specimen can be viewed, processed and analysed.

LSM 710 confocal microscope to use

Zeiss LSM 710 Confocal Microscope

Laser lines

  • 405nm diode
  • 458nm, 488nm, 514nm Argon
  • 543nm Helium/ Neon
  • 633nm Helium/ Neon

Objectives: 10x, 20x, 40x oil DIC, 63x oil DIC, 100x oil, 20x Korr

Stage Inserts: For slides, 35mm dishes or culture plates.

Applications: 2 and 3D imaging; Co-localisation analysis; Live cell imaging; Time series; Multi-position imaging; Photobleaching experiments; Tiling

Software: ZEN 2009

LSM 510 confocal microscope

Zeiss LSM 510 META Confocal Microscope

Laser lines

  • 405nm diode
  • 458nm, 488nm, 514nm Argon
  • 543nm Helium/ Neon
  • 633nm Helium/ Neon

Objectives: 10x, 20x, 40x oil DIC, 63x oil DIC, 100x oil

Stage Inserts: For slides or 35mm dishes.

Applications: 2 and 3D imaging; Co-localisation analysis; Live cell imaging; Time series; Photobleaching experiments

Software: LSM

Spinning Disk Confocal

Details of this new equipment will be available in late 2016.

Laser Microdissection

Zeiss PALM MicroBeam Laser Microdissection

Our P.A.L.M. Microbeam system is available for the microdissection and capture of specified regions from tissue samples for subsequent extraction of DNA, RNA or protein. The system works by a process of laser dissection, followed by pressure catapulting. This provides non-contact sample handling.

Samples can be collected from paraffin-embedded sections, frozen sections or cultured cells. Potential users should be aware that PEN membrane slides and collection tubes with silicone caps are recommended for use on this system.

Both brightfield and fluorescence options are available.

Slide Holder: For 3 slides

Collection device: Accommodates up to eight eppendorf tubes

Objectives: 5x, 10x, 20x, 40x, 63x

Filter sets: DAPI, FITC, Texas Red or equivalent

Camera: AxioCam ICc1

Applications: Dissection and capture of defined tissue regions/cells for subsequent RNA/ DNA/ protein extraction.

Software: PALM Robo v 4.6

PALM laser capture 2



Details of this new equipment will be available in late 2016.

Ariol Scanning System

Allows automated imaging of sections or tissue microarrays (TMAs). Used for the scanning and quantification of both immunohistochemical staining and immunofluorescence.

Nuclear, cytoplasmic and membranous markers can be distinguished and positive staining can be quantified in terms of intensity, size and number of positive events. Vessel density and number can also be analysed for angiogenesis studies.

Microscope:       Olympus BX61

Stage (Prior):     Accommodates up to eight slides

Objectives:        1.25x, 5x for locating sample

                         10x, 20x, 40x 60x for image acquisition

Filter cubes:       DAPI, Spectrum Orange, Spectrum green, Far Red,

                         Spectrum Aqua

Camera:            Olympus iAi

Applications:     Collection and analysis of brightfield or fluorescence; data from sections or TMAs including those stained by fluorescence in situ hybridisation (FISH)

Software:          Dedicated Ariol software


Scanning Facilities

The Pannoramic 250 High Throughput Scanner produces high quality brightfield images with 43X magnification.

Slides can be scanned directly to the server and securely accessed from anywhere in the world. For acquisition of entire tissue sections or microarrays and subsequent analysis using Densito Quant, Nuclear Quant and Membrane Quant image analysis modules. TMA deconvolusion function.

Pannoramic 250 scannerScanner: Pannoramic 250 from 3D Histech

Capacity: 250 slides (25 per rack)

Objective; 20x

Speed: High throughput. Averages 12 slides per hour.

CaseCenter: Can scan directly to server and view from anywhere; can share images with collaborators

Scan profiles: Automatic or manual modes

Applications: Brightfield scanning of whole tissue sections/ TMAs; dedicated software for subsequent analysis

Software: Pannoramic Scanner, Viewer and Analysis modules

Stereo Microscope

This SteREO Lumar. V12 stereo microscope is used for 3D observation and imaging of small objects.

SteREO Lumar V.12 microscopeMicroscope: Zeiss SteREO Lumar. V12

SyCop: System control panel combines joystick, keys and touch screen.

Objectives: S 1.5x and S 0.8x

Halogen: Brightfield, darkfield and DIC

Filter set: DAPI, FITC and TRITC

Camera: Zeiss HRm (monochrome)

Applications: Drosophila studies; Angiogenesis

Software: AxioVision

Timelapse Microscope

Our Zeiss AxiVert 200M time lapse system comprises an inverted, fluorescence microscope with camera and motorised stage. Brightfield and fluorescence detection on live cells. For sequential imaging of multiple, pre-defined locations in a culture plate or on slides over a period of time using the Mark & Find module of AxioVision software.

Axiovert time lapse systemMicroscope: Zeiss AxiVert 200M

Stage: Inserts for slides, culture dishes or multi-well plates

Objectives: 5x, 10x, 20x, 40x

Filter set: FITC, TRITC and Far Red

Camera: AxioCam MRc

Applications: Multi-position time lapse imaging of live cells

Brightfield and/or fluorescence

Software: AxioVision

Our DeltaVision Live Imaging System is high resolution and features an inverted research microscope and fast, high resolution camera. Supplied by Image Solutions (UK), the DeltaVision has a large environment control chamber for live imaging. Our researchers are particularly interested in imaging cell division in detail.

DeltaVision time lapse systemMicroscope: Olympus IX71

Stage: culture dishes

Objectives: 20x, 40x, 60x, 100x

Light sources: White LED Transmitted Light Illuminator

TruLight Fluorescence Illuminator

Filter set: DAPI/ FITC /TRITC/ Far Red

live cell (CFP/YFP and GFP/mCherry).

Camera: CoolSNAP HQ2

Applications: Multi-position time lapse imaging of live cells

Fluorescence Microscopy

Axioplan microscope

Our Zeiss AxioPlan is for brightfield and blue/green/red fluorescence imaging of cells and sections.

Microscope: Upright, epifluorescent microscope

Objectives: 2.5x, 5x, 10x, 20x, 40x, 63X oil

Light source: Halogen and X-Cite

Filter set: DAPI, FITC, and TRITC

Camera: AxioCam MRc

Applications: Imaging fluorescently stained cells or tissue sections; brightfield imaging of immunohistopathology slides

Software: AxioVision


Our Zeiss Axiophot is currently used for brightfield imaging of imuunohistopathology slides although this microscope also has fluorescence capability similar to the Axoioplan.

Axiophot microscope

Microscope: Upright, epifluorescent microscope

Objectives: 2.5x, 5x, 10x, 20x, 40x, 63X oil

Light source: Halogen and HBO

Filter set: DAPI, FITC, and TRITC

Camera: AxioCam HRc

Applications: Brightfield imaging of immunohistopathology slides; Imaging fluorescently stained cells or tissue sections

Software: AxioVision

Analysis Facilities

There are 3 analysis workstations for image processing. The following software is available:

Imaris XT 8.0
Including 8.0 Neuroscience

Count nuclei and cell sorting
Multi Wavelength Cell Scoring
Cell cycle

Dedicated software modules for Pan 250 images
Densito Quant
Nuclear Quant
Membrane Quant

Dedicated software for analysing Ariol scans
Quantification of cytoplasmic, nuclear and membrane staining in sections or Tissue Microarrays
Vessel density and number


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