Microscopy Facility

The Microscopy Facility, mainly located at the Imaging suite, provides a wide portfolio of imaging platforms including Widefield and Confocal microscopes with fast detectors.

Most instruments are suitable for live imaging applications and this includes Selective Plane Illumination Microscopy (SPIM) system used with small animal models or spheroids. The creation of virtual slides through imaging of whole tissue mounts can be achieved with the AxioScanZ.1 slide scanner. In addition, the PALM MicroBeam laser capture microdissection is the perfect precursor for proteomics but will also purify heterogeneous cell cultures and perform localised DNA damage to live cells. Equipment specifications can be obtained from the following sections.

Microscopy Facility Team

Dr Alessandro Di Maio

Microscopy Specialist

Dr Alessandro Di Maio

Alessandro is a cell biologist with an extensive experience in imaging and microscopy (both fluorescence and electron). He received his Ph.D. in 2009 from the NFS Institute (Japan) and University of Pennsylvania (USA). After that, he then joined the Drexel Medical School (USA) for his first postdoc. Subsequently, he was a postdoctoral fellow at UC Santa Barbara (USA). Alessandro moved to the University of Birmingham in 2014, to the Light Microscopy imaging facilities within the College of Life and Environmental Science (2014-2021). Finally in 2021 he moved to the College of Medical and Dental Sciences as Microscopy Specialist of the Microscopy Facility, part of the Medical School Technology Hub. He provides a multidisciplinary service in microscopy science to the academic and non-academic community within the University of Birmingham. 
Email: a.dimaio@bham.ac.uk

Microscopy Specialist

Neal Townsend

Neal Townsend joined Microscopy Facility in June 2022. BSc (hons) in Biomedical Science from University of Kent followed by MSc Microbiology and Infection at University of Birmingham. Following Master’s joined University of Birmingham Turnkey laboratory carrying out Covid-19 PCR testing. Then went on to work in Clinical Immunology Services as a Research Technician before joining the Microscopy Facility, part of the Medical School Technology Hub.
Email: n.j.townsend@bham.ac.uk

Research Facilities Manager

Adriana Flores-Langarica

Email: A.FloresLangarica@bham.ac.uk

Financial Assistant

James Batten

Email: j.batten@bham.ac.uk 

Microscopy Facility Academic Lead

Professor Steve Thomas

Email: s.thomas@bham.ac.uk

Training and Support

We provide training and support for users to independently use all our available equipment available in Stratocore. Currently our training programmes are divided in two sections. Firstly, the CANVAS Module which can be completed at the user pace and once that is completed we deliver an in person training session at the equipment. If you require training just request it in Stratocore. We deliver sessions regularly. 

For our bespoke services, please reach to us to discuss your project and how we can help you.

Access and Booking

External users are encouraged to contact us via email in the first instance, however all internal prospective users will need to request an account on the core facilities booking system Stratocore (unless you already have one). Please ensure you use your UoB email address to register your Stratocore account

As part of your account, you will need a valid finance/grant code. We need this to be able to charge you for your use of the equipment.

You code will either be a project or general ledger. Guidance on finance/grant codes is here:

Project Ledger. (Project Finance Number begins with a ‘1’ or ‘2’). Project Ledger codes require 3 components in the format:

Cost Centre Code       -           Task Number  -           Project Finance Number

C082                           -           1.1                   -           21991

General Ledger. (Project Finance Number begins with a ‘6’). General Ledgers require 2 components in the format:

Cost Centre Code       -           Project Finance Number

C283                           -           65371

If you are unsure about any of your Finance code, contact techubfinance@contacts.bham.ac.uk who will be able to assist you.

Account requests and flow cytometry training requests may be submitted simultaneously.  GCP level users are required to submit a new project form through Stratocore before requesting flow cytometry training.

For any Stratocore or finance relation queries please contact techubfinance@contacts.bham.ac.uk 

Equipment

Zeiss LSM780 Confocal Microscope 

Zeiss LSM 780

The LSM 780 scanner has high sensitivity and is equipped with a 32 element galanium arsenide phosphide (GaAsP) Quasar detector, plus 2 standard PMTs and 1 transmitted light T-PMT. Equipped with a tuneable AOTF and capable of imaging up to 6 channels in multitrack configuration. The AxioObserver.Z1 inverted stand, is equipped with an environmental chamber with CO2 for live cell imaging. Focus stabilisation is through software and hardware based mechanisms. Interchangeable stage inserts for slides, chamber slides, 35mm dishes and multiwall plates. Image capture in 3D and 4D, plus Lambda scanning, and spectral un-mixing capability.

Optics

Objective lensMagnification / NA / ImmersionContrast Method

C-ACHROMAT

10x / 0.45 / Water

 

LD LCI Plan-NEOFLUAR

25x / 0.8 /  Water or Oil

DIC II

Plan-ACHROMAT

40x / 1.2 / Water

DIC III

Plan-APOCHROMAT

63x / 1.2 / Water

DIC III

Plan-APOCHROMAT

63x / 1.4 / Oil

DICIII

Plan-APOCHROMAT

100x / 1.4 / Oil

DIC III

Epifluorescence filter sets

Filter setEx BP nmEm BP nm

Fs49 wf

365

445/50

Fs38 wf

470/40

525/50

Fs43 wf

545/25

635/70

Laser Lines

  • Lasos 30mW Diode 405nm
  • Lasos 25mW LGN3001 multiline Argon, 458, 488, 514nm
  • Lasos 20mW (DPSS 561)   561nm
  • Lasos 2mW   HeNe 594nm
  • Lasos 5mW   HeNe 633nm

Experiment Modes

  • Z stack
  • Multi-positions
  • Time lapse
  • Tile scanning / image stitching of large samples
  • Bleaching

Software and Network Drives

  • Zen 2.1 allows for multidimensional experiment design in 2D, 3D, and 4D
  • PC, HPZ840 4TB 3 RAID Hard drives and 64GB of memory.
  • Desk top script connections to personal offline storage folders 

Location

Imaging Suite, Room WXG86

Zeiss LSM880 Confocal Microscope with Airyscan Fast

 

Zeiss LSM 880

The LSM 880 scanner has high sensitivity and is equipped with a 32 element galanium arsenide phosphide (GaAsP) Quasar detector, plus 2 standard PMTs and 1 transmitted light T-PMT. Equipped with a tuneable AOTF and capable of imaging up to 6 channels in multitrack configuration. The AxioObserver.Z1 inverted stand, is equipped with an environmental chamber with CO2 for live cell imaging. Focus stabilisation is through software and hardware based mechanisms (Definite focus II). Interchangeable stage inserts for slides, chamber slides, 35mm dishes and multiwall plates. Image capture in 3D and 4D, plus Lambda scanning, and spectral un-mixing capability.

lsm 880 with airyscan

Airyscanning

An additional scan detector providing 1.7x isotropic increase in resolution from widefield ~120nm. The Airy Disk or Point spread function from every light emitting point is projected through zoom optics and scanned by a hexagonal array for 32 GaAsP detectors which then undergoes a process of pixel reassignment and subsequent processing.  All dyes and fluorophores that are scanned by the conventional detectors can be Airy-scanned using specific emission filter sets in simultaneous or sequential acquisition modes. 

Airyscanning in Fast mode

In fast mode the beam is shaped to scan not one but 4 lines of pixels in each scanning sweep, acquiring 4x faster than normal Airyscan. Only the central 16 elements of the array are utilised providing a 1.5 x increase in resolution. Excellent for fast imaging of live cell dynamics with increased resolution

lsm 880 with airyscan

ZEISS Webinar: LSM 880 with Airyscan - Revolutionize Your Confocal Imaging
ZEISS LSM 880 with Airyscan: Beam Path and Principle of Airyscanning

Optics

Objective lensMagnification / NA / ImmersionContrast Method

C-ACHROMAT

10x / 0.45 / Water

 

LD LCI Plan-NEOFLUAR

25x / 0.8 /  Water or Oil

DIC II

Plan-ACHROMAT

40x / 1.2 / Water

DIC III

Plan-APOCHROMAT

63x / 1.2 / Water

DIC III

Plan-APOCHROMAT

63x / 1.4 / Oil

DICIII

Plan-APOCHROMAT

100x / 1.4 / Oil

DIC III

Epifluorescence Filter Sets

Filter setEx BP nmEm BP nm

Fs49 wf

365

445/50

Fs38 wf

470/40

525/50

Fs43 wf

545/25

635/70

Airy Scan Emission Filter Sets

BP420-445

+

BP465-505

BP420-480

+

BP495-550

BP495-550

+

LP525

BP495-535

+

LP555

BP495-550

+

LP570

BP570-620 + LP645

Laser Lines

  • Lasos 30mW Diode 405nm
  • Lasos 25mW LGN3001  multiline Argon, 458, 488, 514nm
  • Lasos 20mW (DPSS 561) 561nm
  • Lasos 2mW HeNe 594nm
  • Lasos 5mW HeNe 633nm

Experimental Modes

  • Z stack
  • Multi-positions
  • Time lapse
  • Tile scanning / image stitching of large samples
  • Bleaching and FRET analysis

Software and Network Drives

  • Zen 2.3 allows for multidimensional experiment design in 2D, 3D, and 4D
  • PC, HPZ840 4TB 3 RAID Hard drives and 64GB of memory.
  • Desk top script connections to personal offline storage folders 

Location

Imaging Suite, Room WXG86

Zeiss Lightsheet Z.1 Selective Plane Illumination Microscope

Zeiss Lightsheet Z.1

Unlike the Confocal microscope the Light Sheet microscope illuminates a single, thin plane at one time thus producing an optical section without the need for a confocal pinhole, but increasing SNR significantly. The detection lens is set at 90 degrees to the plane of illumination, and this perpendicular light path and focal plane illumination significantly reduces photo toxicity of delicate samples.

Zeiss Lightsheet Z1 graphic

Application and advantages 

Light sheet fluorescence microscopy is the way to observe small animal models, such as Zebrafish and Drosophila in a more gentle and physiological manner, but is also applicable to Arabidopsis, marine organisms, excised tissue and biopsies.

The sample is usually embedded in agarose and mounted vertically in an imaging chamber via glass a capillary. This allows the sample to be rotated in 360O for optimisation of the light sheet angle, but also to obtain a “Multiview” of a sample for whole organism reconstruction.

The system does not image pixel by pixel but will grab full frame using two sCMOS cameras allowing high resolution time lapse recordings for efficient analysis of dynamics within the sample.

Further background reading including downloads on sample preparation and other protocols

Specification

  • Twin sCMOS PCO Edge 16bit cameras for simultaneous 2 channel acquisition
  • Twin illumination objectives for single or dual sided sample illumination with dual side fusion of the live image
  • Pivot scanning to reduce shadowing
  • Time lapse
  • Multiview
  • Chamber incubation with CO2 available
  • System configured for imaging cleared tissue
  • Objective lenses, 10x 20x and 40x
  • Laser lines, 405,445, 488,514,561 and 638nm
  • 32TB 3 RAID drive processing workstation networked to RDS

Software and Network Drives

  • Zen SP1 Lightsheet,  allows for multidimensional experiment design in 3D, and 4D
  • PC 1, HPZ840 4TB acquisition workstation
  • PC 2, 32TB 3 RAID drive image processing workstation memory.

Location

Imaging Suite, Room WXG89

Zeiss Axio Scan .Z1 Slide Scanner

Zeiss Axioscanner Z1 Slide Scanner

 

Axio Scan .Z1

The fully automated Zeiss Axio Scan .Z1 slide scanner creates high resolution virtual slides of whole tissue sections. Full tissue scanning with automatic or interactive detection of the selected area. The large capacity 100 slide magazine allows for scanning of large batches. Easy slide loading with dedicated imaging frames. Fully adaptable and programmable with synchronised external high speed excitation and internal emission filter wheels. Auto file saving to personalised storage in a secure server location.

 

ZEISS Axio Scan.Z1 - Your Virtual Slide Scanner for High Throughput Whole Slide Imaging

Sample illumination and cameras 

Light SourceCameraPixel size and resolutionFunction

Bright field

LED

3CCD colour 2MP Hitachi 1200x1600 HV-F202SCL

4.4 x 4.4 µm

0.22 µm per pixel*

 

Immunohistochemistry e.g. H&E, HRP, IHC

HXP120 fluorescent white  light

Hamamatsu Orca Flash 4 -4MP 2048x204816bit sCMOS

6.45 x 6.45 µm 0.32 µm / pixel*

 

Multichannel      fluorescence

 

 

 

*20x magnification

 

Optics

Objective lensMagnification / NA

Fluar

5x / 0.25 M27 (course focusing)

Plan-Apochromatic

10x / 0.45 M27

Plan-Apochromatic

20x / 0.8 M27

Plan-Apochromatic

40x/ 0.95 M27

Fluorescence filter sets

Filter setExcitationnmBeam SplitterEmissionnmExamples of fluorophore combinations

Zeiss 49 HE

365

FT385

445/50

Dapi / Hoescht / BV421/ Pacific Blue/ eFluor450 / Alexa 405 / Alexa 350

Zeiss 38 HE

470/40

FT495

525/40

eGFP / YFP / Alexa 488 / FITC / pacific Green / Qdot525 (with ET380nm exciter) / Horizon BV500 / BV510

Zeiss 43 HE

545/25

FT570HE

635/70

Cy3 / Alexa 555/ Rhodamine / pacific Orange / Qdot605 (with ET380nm exciter) / tdTomato / Texas Red / eFLuor605nv / BV605 / Propidium Iodide / PE

Zeiss 64 HE

587/25

FT605HE

647/70

mPlum / Alexa 594 / Alexa 610 / Texas Red / Qdot655 (with ET 380nm exciter) / BV650 /

Chroma ET49006

620/60

ET700/75

700/75

Cy5 / Alexa 633 / 647 / 700 / Qdot705 (with ET380nm exciter)

Slide acceptability and capacity

Single width slide; (max 4 per mounting frame) x 25 width 24-26mm, length 74-76mm, depth 0.8-1.3mm.

Double width slide; (max 2 per mounting frame) x 2 width 52mm, length 74-76mm, depth 0.8-1.3mm.

Quad width slide; (max 1 per frame) width 104mm, length 74-76mm, depth 0.8-1.3mm (optional extra).

Software

ZEN blue (2012) slide scan software has capability to drive whole tissue or multi-region tiling with Z-stacking plus specific profiles for TMA’s and cell spreads etc.

Location

Imaging Suite: Room WXG87

Leica DM6000B upright widefield epifluorescence and colour microscope

Leica DM8000B

The Leica DM6000B is multimodal and equipped with twin Leica cameras for capture in 4 fluorescence channels and colour bright field for histological examination. Based on an upright DM6000B stand with fully motorised stage and filter turret. Applicable for slide analysis only.

Leica Microsystems

Optics

Objective lensMagnification / NA / ImmersionContrast Method

HC Plan Apo

10x / 0.45 / Dry

Phase 1

HC Plan Apo

20x / 0.7 /  Dry

 

Phase 3

Plan Apo

40x / 1.25 / Oil

 

 

Plan Apo

100x / 1.4 / Oil

Phase 3

Epifluorescence filter sets

Filter cubeExcitation nmEmission nmFluorophores

A4

360

Blue 470

Dapi / Hoescht / Pacific Blue / eFluor450 / Alexa Fluor 405

L5

480

Green 527

eGFP / YFP / Alexa 488 / FITC / pacific Green

N3

546

Red 600

Cy3 / Alexa 555/ Rhodamine / pacific Orange / tdTomato / Texas Red / Propidium Iodide / PE

Y5

620

Far Red 700

Cy5 / Alexa 633 / 647 / APC

 

Software and Network Drives

  • Leica LASX core
  • Desk top script connections to personal offline storage folders

Location

Confocal Microscopy Room, Centre for Translational Inflammation Research

Institute of Inflammation and Ageing, QEH/B

Leica DMI6000B widefield epifluorescence and brightfield microscope with timelapse

Leica DMI6000B timelapse

Based in the Centre for Translational Inflammation Research (CTIR), the Leica DMI 6000B is equipped with a DFL350 FX camera for capture in 3 fluorescence channels and bright field. Based on a fully motorised inverted DMI 6000B stand and environmental chamber with CO2 for live cell imaging. A time-lapse module is available for migration studies. Applicable for imaging slides, cell dishes, multi-well plates and chamber slides.

Leica Microsystems

Optics

Objective lensMagnification / NA / ImmersionContrast Method

HCX Pl Fluotar

20x / 0.4 / Corr Dry

Phase 1

HCX Pl Fluotar

40x / 0.6 /  Corr Dry

Phase 2

HCX Pl Fluotar

63x / 0.7 / Corr Dry

Phase 2

 

Filter cubeExcitation nmEmissionnmFluorophores

A4

360

Blue 470

Dapi / Hoescht / Pacific Blue / eFluor450 / Alexa Fluor 405

L5

480

Green 527

eGFP / YFP / Alexa 488 / FITC / pacific Green

N3

546

Red 600

Cy3 / Alexa 555/ Rhodamine / pacific Orange / tdTomato / Texas Red / Propidium Iodide / PE

 

Software and Network Drives

  • Leica LASX core
  • Desk top script connections to personal offline storage folders

Location

Confocal Microscopy Room, Centre for Translational Inflammation Research

Institute of Inflammation and Ageing, QEH/B

Zeiss PALM MicroBeam Laser Capture Microdissection

Zeiss PALM

LCM Is the contamination-free method for separating and collecting cells of interest out of tissue samples mounted on slides or live cell cultures. The isolated pure cell populations are the perfect starting point for specific genetic, proteomic and molecular analysis. PALM MicroBeam makes isolating uncontaminated source material simple, via precise detection of specified areas, and contact free laser microdissection technology, ensuring your results are exact and reproducible. The PALM laser technology can also be used for DNA damage of live cells which can be coupled with live cell time lapse fluorescence imaging of the downstream effects.

Background and introduction to Zeiss PALM LCM

ZEISS Laser Capture Microdissection (LCM): Isolate cells by the force of light
ZEISS Laser Capture Microdissection (LCM): Bridging the Gap between LCM and Proteomics

Microscope stand

  • Axio Observer.Z1 inverted microscope
  • Environmental camber for live cell work
  • Fully motorised stage with joystick
  • Twin CCD cameras for colour brightfield (AxioCamCc1) and greyscale fluorescence (AxioCamMRM)
  • Sample illumination through 100W HBO Mercury epi-fluorescence burner and HAL 100W tungsten transmitted light
  • Sample collection to 200µl and 500µl PCR tubes or Zeiss adhesive caps.

Optics

Objective lensMagnification / NA / ImmersionContrast Method

Fluar

5x / 0.25

 

Fluar

10x / 0.5

 

LD Plan Neofluer

20x / 0.4 / Korr

 

LD Plan Neofluer

40x / 0.6/ Korr

 

EC Plan Neofluer

100x / 1.3 / Oil

 

Plan Apochromat

150x / 1.35 / Oil

DIC

Widefield Epi-fluorescence Dichroic Filter sets

Filter setEx BPnmEm BPnmFluorophores

FS49

365

445/50

Dapi / Hoescht / Pacific Blue / eFluor450 / Alexa Fluor 405

FS38 HE

470/40

525/50

eGFP / YFP / Alexa 488 / FITC / pacific Green

FS20

546/12

575/640

Cy3 / Alexa 555/ Rhodamine / pacific Orange / tdTomato / Texas Red / Propidium Iodide / PE

Software and Network Drives

  • Zeiss PALM Robo software version 4.6
  • Desk top script connections to personal offline storage folders

Location

Imaging Suite: Room WXG87

Zeiss Axio Observer widefield system with Apotome 2.0 system

Zeiss Axio w apotome IBR

Motorised Axio Observer geared toward fluorescence performance with LED Colibri.2 illumination system that offers high speed switching times to the order of less than 1 ms. The unique feature of the Colibri.2 design in comparison with all other LED systems currently available is its unmatched homogeneity. The light path up to the illuminator output is the same for each LED module independent of its installation position. Four channels are included at 365nm, 470nm, 565nm, and 590nm. The system is equipped with an Hamamatsu ORCA Flash 4.0 for high speed and high sensitivity.

In addition, the system is equipped with the Apotome.2 Confocal Structured Illumination device for creating optical sections with high contrast. Despite the magnification used, the ApoTome.2 automatically places the right grid in the beam path of the microscope. Reduction of unwanted background fluorescence increases with the grid frequency and the optical sections become thinner. Structures from outside of the focal plane are suppressed improving contrast and resolution of the optical section.

Contact us

imaging-suite@contacts.bham.ac.uk

techubfinance@contacts.bham.ac.uk

Research Facilities Manager

Dr Adriana Flores-Langarica
Email: A.FloresLangarica@bham.ac.uk

Microscopy Facility Academic Lead

Professor Steve Thomas
Email: s.thomas@bham.ac.uk