Microscopy Hardware & Software

Note for users

For external users, please contact the IMB Microscopy team.

For internal users, please click here to book equipment or request training.

Confocal microscopy is an advanced light microscopy method which utilises a ‘pinhole’ to eliminate out of focus light and is suitable for both live and fixed cells and tissues. The advantage of a confocal microscope over conventional wide-field microscopes is that discrete optical sections can be collected whereby out of focus light can be eliminated. Because of this, high powered lasers are used to illuminate the sample in order to collect enough light only from the desired focal plane.

Focused beams of laser light are scanned across the sample (Laser Scanning Microscopy, LSM) and light only from the desired focal plane is allowed to enter the detector. Depending on the fluorophores in your sample, and the number of detectors available, multiple fluorophores can be excited and detected simultaneously. Traditional detectors are photo-multiplier tubes, however more recent Gallium Arsenide Phosphide (GaAsP) detectors have been developed to increase sensitivity (Confocal 4, Airyscan; Confocal 5, BiG detectors).

These microscopes provide excellent axial resolution, and very high signal to noise sampling, however this often comes with a sacrifice in temporal resolution due to the slow nature of scanning pixel-by-pixel across the image during capture. Some systems overcome this speed issue with either faster scanners (Leica SP8, resonant scanners) or with multiple pinholes (Spinning Disc Confocal, Yokogawa CSU-X1) microscopes overcome this speed limitation in unique ways.

Confocal 3 - Upright LSM 710 Meta

Resource Links:


Room 6.019b - Zeiss Axiovert 200 Inverted Microscope Stand with LSM 710 Meta Confocal Scanner

Upright point-scanning laser confocal microscope with spectral detection  Suited for imaging fixed samples on slides, samples with low fluorescence and live imaging.

Features Include:

  • Fully motorised X-Y-Z stage
  • Tiled imaging
  • Multi-position imaging
  • Spectral imaging

 

Transmitted Light:  Zeiss 100W Halogen Lamp

Reflected Light:  Exfo Xcite 120W White Light Lamp

Condensor:

Name N.A. W.D. mm Position 1 Position 2 Position 3 Position 4 Position 5 Position 6
- - - - - - - - -

Objectives:

Position Objective Magnification N.A. Immersion W.D. (mm) Type Type Thread
1 Plan Apochromat 10x 0.45 Dry - -   M27
2 Plan Apochromat 20x 0.80 Dry - - - M27
3 Plan Apochromat 40x 1.3 Oil - -   M27
4 Plan Apochromat 63x 1.4 Oil - -   M27

 

Fluorescent Filter Sets:

Position Name Excitation Dichroic Emission Suitable Dyes
1 Zeiss #63 HE 572/25 FT 590 629/62 mCherry, Texas Red
2 Zeiss #38 HE 470/40 FT 495 525/50 EGFP, Alexa Fluor 488
3 Zeiss #47 HE 436/25 FT 455 480/40 DAPI, Hoechst
4 - - - - -
5 - - - - -

 

Lasers:

Laser

Wavelength

Laser Power

BFP Power*

Suitable Dyes

405

405nm

-

-

DAPI / Hoechst

Argon Ion

458nm

- -

CFP

Argon Ion

488nm

- -

GFP / Alexa Fluor488

Argon Ion

514nm

- -

YFP

561

561nm

- -

mCherry / Cy3

633

633nm

- -

Cy5 / A647

*BFP = Back Focal Plane of Objective

 

Computer:

Fujitsu PC - 3GHz Xeon Processor - 32GB RAM - 1GB nVidia Quadro GPU

3TB Raid Array

30" LCD Monitor

 

Software: 

Zeiss Zen 2012 Black

 

Accessories:

Incubation chamber with CO2 and Temperature control

Confocal 4 - Inverted LSM 710 Meta NLO AiryScan

Resource Links:


Room 6.034a - Zeiss Axiovert 200 Inverted Microscope Stand with LSM 710 Meta Confocal Scanner

Inverted point-scanning laser confocal microscope with spectral detection and Airyscan super resolution detector. 2-photon imaging with Mai Tai eHP 760-1040nm laser with dedicated BiG(GaAsP) detectors. Suited for imaging fixed samples on slides, samples with low fluorescence and live imaging.

Features Include:

  • Fully motorised X-Y-Z stage
  • Piezo Z-drive for rapid Z-stacks
  • High-sensitivity BiG detectors (GFP/mCherry) for 2-photon imaging
  • AiryScan detector for super resolution imaging to 130nm (XY)
  • CO2 and temperature incubation for live cells and tissue
  • Tiled imaging
  • Multi-position imaging
  • Spectral imaging

Transmitted Light:  Zeiss 100W Halogen Lamp

Reflected Light:  Exfo Xcite 120W White Light Lamp

Condensor:

Name N.A. W.D. mm Position 1 Position 2 Position 3 Position 4 Position 5 Position 6
Universal LWD 0.55 26 - - - - - -

Objectives:

Position Objective Magnification N.A. Immersion W.D. (mm) Type Type Thread
1 Plan Apochromat 20x 0.8 Dry - -   M27
2 Plan Apochromat 40x 1.3 Oil - -   M27
3 Plan Apochromat 63x 1.40 Oil - -   M27
4 Plan Apochromat 100x 1.46 Oil - -   M27
5 - - - - - -   M27
6 Plan Apochromat 10x 0.45 Dry - -   M27

 

Fluorescent Filter Sets:

Position Name Excitation Dichroic Emission Suitable Dyes
1

Zeiss #63 HE

572/25

FT 590

629/62

mCherry, Texas Red

2

Zeiss #38 HE

470/40

FT 495

525/50

EGFP, Alexa Fluor 488

3

Zeiss #47 HE

436/25

FT 455

480/40

DAPI, Hoechst

4 - - - - -
5 - - - - -

 

Lasers:

Laser

Wavelength

Laser Power

BFP Power*

Suitable Dyes

405

405nm

20mW

4.5mW

DAPI / Hoechst

Argon Ion

458nm

1mW

0.4mW

CFP

Argon Ion

488nm

20mW

8mW

GFP / A488

Argon Ion

514nm

3mW

1mW

YFP

561

561nm

10mW

5mW

mCherry / Cy3

633

633nm

5mW

1mW

Cy5 / A647

Mai Tai

780 - 1040 nm

2000mW

10mW - 50mW

2 Photon Dyes

*BFP = Back Focal Plane of Objective

 

Computer:

Fujitsu PC - 3GHz Xeon Processor - 32GB RAM - 1GB nVidia Quadro GPU

3TB Raid Array

30" LCD Monitor

 

Software:

Zeiss Zen 2012 Black

 

Accessories:

Incubation chamber with CO2 and Temperature control

Confocal 5 - Inverted LSM 710 Meta BIG

Resource Links:


Room 6.028 - Zeiss Axiovert 200 Inverted Microscope Stand with LSM 710 Meta Confocal Scanner

Inverted point-scanning laser confocal microscope with spectral detection and Airyscan super resolution detector. 2-photon imaging with Mai Tai eHP 760-1040nm laser with dedicated BiG(GaAsP) detectors. Suited for imaging fixed samples on slides, samples with low fluorescence and live imaging.

Features Include:

  • Fully motorised X-Y-Z stage
  • High-sensitivity BiG detectors (GFP/mCherry and CFP/YFP) 
  • CO2 and temperature incubation for live cells and tissue
  • Tiled imaging
  • Multi-position imaging
  • Spectral imaging

 

Transmitted Light:  Zeiss 100W Halogen Lamp

Reflected Light:  Exfo Xcite 120W White Light Lamp

Condensor:

Name N.A. W.D. mm Position 1 Position 2 Position 3 Position 4 Position 5 Position 6
Universal LWD 0.55 26 - - - - - -

Objectives:

Position Objective Magnification N.A. Immersion W.D. (mm) Type Type Thread
1 Plan Apochromat 10x 0.45 Dry - -   M27
2 Plan Epiplan-Neofluar 20x 0.5 Dry - DIC   M27
3 EC Plan-Neofluar 40x 0.75 Dry - -   M27
4 LD C-Apochromat 40x 1.1 Water - -   M27
5

LD C-Apochromat

63x 1.15 Water - -   M27

 

Fluorescent Filter Sets:

Position Name Excitation Dichroic Emission Suitable Dyes
1

Zeiss #63 HE

572/25

FT 590

629/62

mCherry, Texas Red

2

Zeiss #38 HE

470/40

FT 495

525/50

EGFP, Alexa Fluor 488

3

Zeiss #47 HE

436/25

FT 455

480/40

DAPI, Hoechst

4 mCherry LP 560/20 580LP 585LP mCherry, Cy3
5

-

- - -

-

6

-

- - -

-

 

Lasers:

Laser

Wavelength

Laser Power

BFP Power*

Suitable Dyes

405

405nm

-

-

DAPI / Hoechst

Argon Ion

458nm

-

-

CFP

Argon Ion

488nm

-

-

GFP / A488

Argon Ion

514nm

-

-

YFP

561

561nm

-

-

mCherry / Cy3

594

594nm

-

-

A594

633

633nm

-

-

Cy5 / A647

*BFP = Back Focal Plane of Objective

 

Computer:

Fujitsu PC - 3GHz Xeon Processor - 32GB RAM - 1GB nVidia Quadro GPU

3TB Raid Array

30" LCD Monitor

 

Software: 

Zeiss Zen 2012 Black

 

Accessories:

Incubation chamber with CO2 and Temperature control

 

Leica STED Confocal - Inverted SP8 STED 3X

Current Status:  Fully Operational


Resource Links:


Room 6.029a - Leica DMi8 Inverted Microscope Stand with SP8 Galvo and Resonant Confocal Scanners, White Light Laser (WLL), STED 3X super-resolution, and FLIM/FRET

Inverted point-scanning laser confocal microscope with spectral, super resolution and FLIM/FRET detection. Tuneable 470nm - 670nm WLL, 2 x PMT and 2 x HyD detectors. Suited for imaging fixed samples on slides, samples with low fluorescence and live imaging.

Features Include:

  • Fully motorised X-Y-Z stage
  • High-sensitivity HyD detectors 
  • CO2 and temperature incubation for live cells and tissue
  • Tiled imaging
  • Multi-position imaging
  • Spectral imaging
  • Super-Resolution Imaging with 592nm, 660nm and 775nm STED lasers
  • Fast Resonant Imaging
  • FLIM/FRET Imaging with WLL and 440nm pulsed lasers

 

Transmitted Light:  Leica LED Lamp

Reflected Light:  Leica EL6000 120W White Light Lamp

Condensor:

Name N.A. W.D. mm Position 1 Position 2 Position 3 Position 4 Position 5 Position 6
Universal LWD 0.55 28 - K3 K6 K7 - -

Objectives:

Position Objective Magnification N.A. Immersion W.D. (mm) Type Type Thread
1 HC Plan Apochromat 10x 0.4 Dry 2.2 DIC    
2 HC Plan Apochromat 20x 0.75 Multi 0.67 DIC    
3 HC Plan Apochromat 40x 1.1 Water 0.65 DIC    
                 
5

HC Plan Apochromat

93x 1.30 Glyc 0.3 DIC    
6 HC Plan Apochromat 100x 1.40 Oil 0.13 DIC    

 

Fluorescent Filter Sets:

Position Name Excitation Dichroic Emission Suitable Dyes
1

DAPI

350/50

 

460/50

DAPI, Hoechst

2

GFP

470/40

 

525/50

EGFP, A488

3

YFP

500/20

 

535/30

YFP

4 Texas Red 560/40   630/75 Texas Red, mCherry
           

 

Lasers:

Laser

Wavelength

Laser Power

BFP Power*

Suitable Dyes

405

405nm

50mW

-

DAPI / Hoechst

440 pulsed

440nm

-

-

CFP FLIM/FRET

442

442nm 40mW - CFP
WLL

470nm-670nm

1.5mW

-

Visible Dyes

92 STED

592nm

1.5W

-

Star 488, Oregeon Green

660 STED

660nm

1.5W

-

Star 470sx, A546

775 STED

775nm

1.5W

-

SiR

*BFP = Back Focal Plane of Objective

 

Computer:

HP Z640 PC - 3GHz Xeon Processor - 64GB RAM - 24GB nVidia Quadro M6000 GPU

3TB Raid Array

2 x 30" LCD Monitor

 

Software: 

Leica LASX Software

Co-localisation, 3D visualisation, FRAP, FRET, SymphoTime FLIM

 

Accessories:

Incubation chamber with CO2 and Temperature control

 

Spinning Disc Confocal - Inverted Cell Observer SD

Resource Links:


Room 6.029 - Zeiss Axiovert 200 Inverted Microscope Stand with CSU-X1 scanhead

Inverted spinning disc laser confocal microscope  Suited for live imaging.

Features Include:

  • Fully motorised X-Y-Z stage
  • Piezo Z-drive for rapid Z-stacks
  • CO2 and temperature incubation for live cells and tissue
  • Tiled imaging
  • Multi-position imaging

Transmitted Light:  Zeiss 100W Halogen Lamp

Reflected Light:  Exfo Xcite 120W White Light Lamp

Condensor:

Name N.A. W.D. mm Position 1 Position 2 Position 3 Position 4 Position 5 Position 6
Universal LWD 0.45 54 Open PhL Ph1 Ph2 DIC I DIC II

Objectives:

Position Objective Magnification N.A. Immersion W.D. (mm) Type Type Thread
1 Plan Apochromat 40x 0.95 Dry - DIC III - M27
2 C Apo 40x 1.2 Water - DIC III   M27
3 LCI PlanN 63x 1.3 Water - DIC III   M27
4 Plan Apochromat 10x 0.45 Dry - DIC II   M27
5 Plan Apochromat 20x 0.8 Dry - DIC II   M27
6

-

-

-

-

-

-

 

-

Eyepiece Fluorescent Filter Sets:

Position Name Excitation Dichroic Emission Suitable Dyes
1 CFP (47HE) 436/25 455 480/40 ECFP, Cerulean
2 GFP (38HE) 470/40 495 525/50 EGFP, Alexa Fluor 488
3 YFP (46HE) 500/25 515 535/30 EYFP, Citrine
4 RFP (63HE) 572/25 590 629/62 mCherry, Cy3
5 - - - - -
6

-

- - - -

Confocal Fluorescence Filter Sets:

First Dichroic

Second Dichroic Camera1 Camera2

405/488/561

Empty 485/30 562/45
457/514/647 510LP 535/30 630/98
405/488/561/647 560LP - -

Computer:

Fujitsu PC - 3GHz Xeon Processor - 32GB RAM - 1GB nVidia Quadro GPU

3TB Raid Array

30" LCD Monitor

Software: 

Zeiss Zen 2012 Blue

Accessories:

Incubation chamber with CO2 and Temperature control

Wide-field microscopy involves illumination of the whole sample, and relies on the optical characteristics of the imaging system to capture a single focal plane. The limitation of these kinds of imaging systems is that often, out of focus light (from differing sample planes) are captured in your images, resulting in image-blur. This image blur will lower your signal to noise, which is the contrast of your images. One way to overcome this is by using specialised optics with very narrow depths of field (High NA objectives) coupled with computational algorithms that can correct for out of focus light, this process is called deconvolution.

The light coming from your sample scatters (diffraction) in all directions when illuminated, and this can be affected by coverslip thickness, sample mounting medium and the many components of the microscope between your sample and the camera. The way that the light diffracts can be characterised by the point spread function (PSF) whereby a single point of light of known size (fluorescent bead) is captured in xyz and shows the scattering behaviour of light in all dimensions for that particular optical system. The PSF is then used to reverse the effects of out of focus light by correcting for these known distortions in all dimensions.

The PSF can be generated for your particular sample using a fluorescent bead that is smaller than the smallest resolvable structure by the particular imaging system, or it can be theoretically generated using known algorithms. Two main deconvolution algorithms exist, the Richardson-Lucy and Wiener deconvolution algorithms. Deconvolution is an iterative process which is cycled on your images. Deconvolution is a post processing method, and is available either on the microscope (Deltavision, Nikon Deconvolution Microscope) or via software (Analysis Computers, Microvolution, AutoQuant).

Deltavision

Resource Links:


Room 6.025b - Olympus IX80 Inverted Microscope Stand with Photometrics Coolsnap HQ2 camera

Inverted widefield microscope with Lumencor 7 line LED lightsource, high speed filter wheels and CCD camera. Suited for imaging fixed samples on slides, samples with low fluorescence and live imaging.

Features Include:

  • Fully motorised X-Y-Z stage
  • High Speed Z-drive for rapid Z-stacks
  • CO2 and temperature incubation for live cells and tissue
  • Tiled imaging
  • Multi-position imaging

Transmitted Light100W LED Lamp

Reflected Light:  Lumencor Spectra LED Lightsource

Condensor:

Name N.A. W.D. mm Position 1 Position 2 Position 3 Position 4 Position 5 Position 6
Universal LWD 0.45 54 Open PhL Ph1 Ph2 DIC I DIC II

Objectives:

Position Objective Magnification N.A. Immersion W.D. (mm) Type Type Thread
1 U-Apochromat 40x 1.35 Oil - DIC   M27
2 Plan Apochromat 60x 1.35 Oil - DIC   M27
3 UPLS-Apochromat 100x 1.4 Oil - DIC   M27
4 - - - - - -    
5 - - - - - -    
6 - - - - - -    

Fluorescent Filter Sets:

Position Name Excitation Dichroic Emission Suitable Dyes
1 DAPI 360/40 Quad Band 457/40 DAPI, Hoechst
2 FITC 490/20 Quad Band 526/38 EGFP, Alexa Fluor 488
3 TRITC 555/28 Quad Band 617/63 mCherry, Alexa Fluor 555
4 Cy5 640/20 Quad Band 685/40 Cy5, Alexa Fluor 647

LEDs:

Laser

Wavelength

Laser Power

BFP Power*

Suitable Dyes

390

390nm

20mW

4.5mW

DAPI / Hoechst

440

440nm

5mW

1mW

CFP

485

485nm

20mW

8mW

GFP / A488

514

514nm

3mW

1mW

YFP

563

563nm

10mW

5mW

mCherry / Cy3

594

594nm

5mW

1mW

A594

640

640nm

5mW

2mW

Cy5 / A647

*BFP = Back Focal Plane of Objective

Computer:

Dell PC - 3GHz Xeon Processor - 32GB RAM - 1GB nVidia Quadro GPU

1TB Raid Array

30" LCD Monitor

Software: 

Softworx

Accessories:

Incubation chamber with CO2 and Temperature control

Nikon Deconvolution

Resource Links:


Room 6.025c - Nikon Ti-E Inverted Microscope Stand with Hamamatsu Flash 4.0 sCMOS camera

Inverted widefield microscope with Lumencor 7 line LED lightsource, high speed filter wheels and CMOS camera. Suited for imaging fixed samples on slides, samples with low fluorescence and live imaging.

Features Include:

  • Fully motorised X-Y-Z stage
  • Piezo Z-drive for rapid Z-stacks
  • CO2 and temperature incubation for live cells and tissue
  • Tiled imaging
  • Multi-position imaging
  • Transmitted Light:  Sutter 100W LED Lamp

Reflected Light:  Lumencor Spectra LED Lightsource

Condensor:

Name N.A. W.D. mm Position 1 Position 2 Position 3 Position 4 Position 5 Position 6
Universal LWD 0.45 54 - - - - - -

Objectives:

Position Objective Magnification N.A. Immersion W.D. (mm) Type Type Thread
1 Plan Apochromat 4x 0.2 Dry - -   M27
2 Plan Apochromat 10x 0.45 Dry 4 DIC   M27
3 Plan Apochromat 20x 0.75 Dry 1 DIC   M27
4 Plan Apochromat 40x 0.95 Dry 0.25 DIC   M27
5 S Fluor 40x 1.30 Oil 0.22 DIC   M27
6 Plan Apochromat 60x 1.4 Oil 0.13 DIC   M27

 

Fluorescent Filters:

Excitation Dichroic Emission
390/18 410/504/582/669 440/521/607/700
438/24 462/523 440/40
485/20 505/606 479/40
513/17 436/514/604 525/30
560/25 488LP 542/27
585/29   631/36
650/13   607/36
    692/40
    488LP

 

LEDs:

Designation

Wavelength

Power

BFP Power*

Suitable Dyes

390

390nm

-

-

DAPI / Hoechst

440

440nm

-

-

CFP

485

485nm

-

-

GFP / A488

514

514nm

-

-

YFP

563

563nm

-

-

mCherry / Cy3

594

594nm

-

-

A594

640

640nm

-

-

Cy5 / A647

*BFP = Back Focal Plane of Objective

Computer:

Dell PC - 3GHz Xeon Processor - 32GB RAM - 1GB nVidia Quadro GPU

3TB Raid Array

30" LCD Monitor

Software: 

NIS Elements 4.3

Accessories:

Incubation chamber with CO2 and Temperature control

OBS

Room 6.018 - Olympus IX81 Inverted Microscope Stand with Hamamatsu Orca CCD camera

Inverted widefield microscope with Xenon lightsource, high speed filter wheels and CCD camera. Suited for imaging fixed samples on slides, samples with low fluorescence and live imaging.

Features Include:

  • Fully motorised X-Y-Z stage
  • CO2 and temperature incubation for live cells and tissue
  • Tiled imaging
  • Multi-position imaging

Transmitted Light:  Olympus 100W Halogen Lamp

Reflected Light:  Olympus MT20 Xenon White Lightsource

Condensor:

Name N.A. W.D. mm Position 1 Position 2 Position 3 Position 4 Position 5 Position 6
Universal LWD 0.45 54 Open PhL Ph1 Ph2 DIC I DIC II

Objectives:

Position Objective Magnification N.A. Immersion W.D. (mm) Type Type Thread
1 Plan Apochromat 10x 0.4 Dry - DIC   M27
2 Plan Apochromat 20x 0.75 Dry - DIC   M27
3 Plan Apochromat 40x 1.0 Oil - DIC   M27
4 Plan Apochromat 60x 1.35 Oil - DIC   M27

 

Fluorescent Filter Sets:

Position Name Excitation Dichroic Emission Suitable Dyes
1 GFP/RFP S500/20 dual band dual band GFP, RFP, mCherry
2 CFP/YFP S430/25

dual band

dual band

CFP, YFP
3   S565/55      
4   S470/30      

 

Computer:

Dell PC - 3GHz Xeon Processor - 8GB RAM - 256GB nVidia Quadro GPU

1TB Raid Array

30" LCD Monitor

 

Software: 

Cell^R

 

Accessories:

Incubation chamber with CO2 and Temperature control

 

Lattice Lighsheet Microscope

Room 6.019B

The Lattice Lightsheet microscope is an advanced live cell microscope developed by Nobel Prize winner Eric Betzig in 2014. This microscope is extremely gentle on cells allowing for very long acquisitions, as well as being super-fast, (capturing full 3D volumes in under a second).

Highlights

  • Very High spatial resolution (230 nm, 230 nm, 300 nm, xyz)
  • Very High Temporal resolution (100 slices / second)
  • Very low photo-toxicity
  • Opportunity to generate very rare data (very few working systems world wide)
  • 4 Individual lasers (440 nm (CFP), 488 nm (GFP), 560 nm (RFP), 640 nm (Far Red))

Challenges

  • Massive data sets are generated by this system (terabytes)
  • Visualisation and analysis software solutions are not equipped for large volumes of LLSM data, instead MIPS are generated for indexing of files, and finding sections of movies for further analysis. Large collaborations are underway to develop tools to fix this.
  • This system is not a ‘turnkey solution’ like our Zeiss systems, therefore the software is not as refined, and often many alignments are required to optimise the imaging output.

Sample Preparation

  • This microscope takes 5 mm coverslips (thickness is not important) mounted on the holder shown below.
  • The stage can be moved within a 3 x 3 mm region from the centre of the coverslip
  • Samples must be adhered to the coverslip (for non-single cell imaging please consult with facility staff)
  • Samples are imaged with water dipping lens’ with your sample in a 8 mL water bath (take this into account if your require stimulants/drugs in your imaging media)
  • The stage/water-bath is heated, however CO2 is not available while imaging.
  • The LLSM room has an incubator set to 37 oC 5% CO2.

BrightField/DarkField (BF/DF)

Current Status:  Fully Operational


Resource Links:


Room 4.022 - Olympus BX51 Upright Microscope Stand with Olympus DP70 CCD camera

Upright widefield microscope with Halogen lightsource and CCD camera. Suited for imaging fixed samples on slides.

Features Include:

  • Manual X-Y-Z stage

Transmitted Light:  Olympus 100W Halogen Lamp

Condensor:

Name N.A. W.D. mm
Brightfield 0.90 -

Objectives:

Position Objective Magnification N.A. Immersion W.D. (mm) Type Type Thread
1

PlanN

2x

0.06

Dry

-

-

 

M27

2

UPlanApo

4x

0.16

Dry

-

-

 

M27

3

PlanN

10x

0.25

Dry

-

-

 

M27

4

UplanSApo

20x

0.75

Dry

-

-

 

M27

5

UPlanSApo

40x

0.90

Dry

-

-

 

M27

6

-

-

-

-

-

-

 

M27

Computer:

Dell PC - 3GHz Xeon Processor - 8GB RAM - 256GB nVidia Quadro GPU

1TB Raid Array

30" LCD Monitor

Software: 

DP Manager

 

Fluoro 1

Current Status:  Fully Operational


Resource Links:


Room 4.022 - Olympus BX51 Upright Microscope Stand with Olympus DP70 CCD camera

Upright widefield microscope with Mercury lightsource and CCD camera. Suited for imaging fixed and live fluorescent samples.

Features Include:

  • Manual X-Y-Z stage
  • Polarised light
  • Differential Interference Contrast (DIC)
  • Optovar (1x, 1.25x, 1.6x, 2x)

Transmitted Light:  Olympus 100W Halogen Lamp

Reflected Light:  Olympus 100W Mercury White Lightsource

Condensor:

Name N.A. W.D. mm Position 1 Position 2 Position 3 Position 4 Position 5 Position 6

Position 7

Position 8

Universal 0.9 - Open Open Open 10x DIC 20x DIC 40x DIC 60x DIC 100x DIC

Objectives:

Position Objective Magnification N.A. Immersion W.D. (mm) Type Type Thread
1 Plan Apochromat 2x 0.08 Dry - -   M27
2 Plan Apochromat 10x 0.40 Dry - -   M27
3 Plan Apochromat 20x 0.75 Dry - -   M27
4 UApo 40x 1.35 Oil - -   M27
5 Plan Apochromat 60x 1.35 Oil - -   M27
6 Plan Apochromat 100x 1.4 Oil - -   M27

Fluorescent Filter Sets:

Position Name Excitation Dichroic Emission Suitable Dyes
1 DAPI - 5060C 377/50 409LP 447/60 DAPI, Hoechst
2 GFP-4050A 466/40 495LP 525/50 EGFP, Alexa Fluor 488
3 mCherry-40LP-A 562/40 593LP 593LP

mCherry, Alexa Fluor 568

4 CFP-2432C 438/24 458LP 483/32 ECFP, mCerulean
5 YFP-2427B 500/24 520LP 542/27 EYFP, mVenus
6 Empty - - - Brightfield

Computer:

Dell PC - 3GHz Xeon Processor - 8GB RAM - 256GB nVidia Quadro GPU

1TB Raid Array

30" LCD Monitor

Software: 

DP Manager, DP Controller

Fluoro 3 - Inverted Olympus IX70

Current Status:  Fully Operational


Resource Links:


Room 2.138 - Olympus IX70 Inverted Microscope Stand with Nikon DS-Fi1 CCD camera

Inverted widefield microscope with Mercury lightsource and CCD camera. Suited for imaging fixed and live fluorescent samples.

Features Include:

  • Manual X-Y-Z stage

Transmitted Light:  Olympus 100W Halogen Lamp

Reflected Light:  XCite 120Q Halogen White Lightsource

Condensor:

Name N.A. W.D. mm Position 1 Position 2 Position 3 Position 4 Position 5 Position 6
Universal LWD 0.45 54 Open PhL Ph1 Ph2 DIC I DIC II

Objectives:

Position Objective Magnification N.A. Immersion W.D. (mm) Type Type Thread
1 Plan Apochromat 4x 0.5 Dry 2 PhL ADL M27
2 Plan Apochromat 10x 0.75 Dry 0.5 Ph1   M27
3 Plan Apochromat 20x 0.75 Dry 0.4 Ph2 ADL M27
4 Plan Apochromat 40x 0.95 Dry 0.2 DIC I   M27
5 Plan Apochromat 63x 1.4 Oil 0.17 DIC II   M27
6 Plan Apochromat 100x 1.4 Oil 0.13 DIC III   M27

Fluorescent Filter Sets:

Position Name Excitation Dichroic Emission Suitable Dyes
1 DAPI - 5060C 377/50 409LP 447/60 DAPI, Hoechst
2 CFP - 2432C 438/24 458LP 483/32 CFP, Cerulean
3 GFP-3000B 488/10 505LP 530/60 GFP, A488
4 mCherry LP 560/20 580LP 585LP mCherry, Cy3
5   - - -  
6   - - -  

Computer:

Dell PC - 3GHz Xeon Processor - 8GB RAM - 256GB nVidia Quadro GPU

1TB Raid Array

30" LCD Monitor

Software: 

NIS Elements

Fluoro 4 - Inverted Nikon Ti-U

Current Status:  Fully Operational


Resource Links:


Room 6.025a - Nikon Ti-U Inverted Microscope Stand with Nikon DS-Fi1 and Qi1 CCD cameras

Inverted widefield microscope with Mercury lightsource and CCD camera. Suited for imaging fixed and live fluorescent samples.

Features Include:

  • Manual X-Y-Z stage

Transmitted Light:  Nikon 100W Halogen Lamp

Reflected Light:  Nikon 100W Mercury White Lightsource

Condensor:

Name N.A. W.D. mm Position 1 Position 2 Position 3 Position 4 Position 5 Position 6
Universal LWD 0.45 54 Open PhL Ph1 Ph2 DIC I DIC II

Objectives:

Position Objective Magnification N.A. Immersion W.D. (mm) Type Type Thread
1 Plan Fluor 4x 0.13 Dry - PhL DL M27
2 Plan Fluor 10x 0.30 Dry - Ph1 DL M27
3 Plan Fluor ELWD 20x 0.45 Dry - Ph1 ADL M27
4 Plan Fluor ELWD 40x 0.60 Dry - Ph2 ADL M27
5 Plan Fluor 100x 1.30 Oil - Ph3 DDL M27
6 - - - - - - - M27

Fluorescent Filter Sets:

Position Name Excitation Dichroic Emission Suitable Dyes
1 DAPI - 5060C 377/50 409LP 447/60 DAPI, Hoechst
2 CFP - 2432C 438/24 458LP 483/32 ECFP, Cerulean
3 GFP-3000B 488/10 505LP 530/60 EGFP, Alexa Fluor 488
4 YFP-2427B 500/24 520LP 542/27 EYFP, mVenus
5 mCherry-40LP-A 562/40 593LP 593LP mCherry Alexa Fluor 568
6 Empty - - - Brightfield

Computer:

Dell PC - 3GHz Xeon Processor - 8GB RAM - 256GB nVidia Quadro GPU

1TB Raid Array

30" LCD Monitor

Software: 

NIS Elements-BR, NIS Elements F

Accessories:

Motorised Z-Focus

Fluoro 5 - Upright Zeiss AxioImager

Current Status:  Fully Operational


Resource Links:


Room 3.011 - Zeiss AxioImage M2.m Microscope Stand with Apotome2 and Axiocam 506 camera

Inverted widefield microscope with Mercury lightsource and CCD camera. Suited for imaging fixed and live fluorescent samples.

Features Include:

Motorised X-Y-Z stage, Apotome2

Transmitted Light:  LED illumination

Reflected Light:  HXP 120c White Lightsource

Condensor:

Name N.A. W.D. mm Position 1 Position 2 Position 3 Position 4 Position 5 Position 6
Motorised Universal 0.9     DIC I DIC II DIC III    

Objectives:

Position Objective Magnification N.A. Immersion W.D. (mm) Type Type Thread
1 EC Plan NeoFluar 5x 0.16 Dry 18.5 DIC   M27
2 Plan Apochromat 10x 0.30 Dry 2 DIC   M27
3 Plan Apochromat 20x 0.80 Dry 0.55 DIC   M27
4 Plan Neofluar 40x 1.30 Oil 0.21 DIC   M27
5 Plan Apochromat 63x 1.40 Oil 0.14 DIC   M27
6 Plan Apochromat 100x 1.40 Oil 0.17 DIC   M27

 

Fluorescent Filter Sets:

Position Name Excitation Dichroic Emission Suitable Dyes
1 DAPI 49 365 395 445/50 DAPI, Hoechst
2 FITC 44 475/40 500 530/50 EGFP, Alexa Fluor 488
3 Cy3 43 545/25 570 605/70 Cy3
4 Texas Red 45 560/40 585 630/75 Tx Red, mCherry, A568
5 Cy5 50 640/30 660 690/50 Cy5, A647
6 Empty - - - Brightfield

 

Computer:

HP Z820 PC - 3GHz Xeon Processor -64GB RAM - 1GB ATI Firepro V5800 GPU

1TB Raid Array

30" LCD Monitor

 

Software: 

Zeiss Zen 2 with Tiling and EDF modules

Accessories:

BD Pathway1&2

Current Status:  Fully Operational


Resource Links:


Room 6.033 - Custom Inverted Microscope Stand with Hamamatsu Orca CCD camera

Inverted widefield microscope with Dual Mercury lightsources, high speed filter wheels and CCD camera. Suited for imaging fixed samples on slides, samples with low fluorescence and live imaging.

Features Include:

  • Fully motorised X-Y-Z stage
  • CO2 and temperature incubation for live cells and tissue
  • Tiled imaging
  • Multi-position imaging

Transmitted Light10W LED Lamp

Reflected Light:  Olympus Mercury White Lightsource

Objectives:

Position Objective Magnification N.A. Immersion W.D. (mm) Type Type Thread
1 Plan Apochromat 4x 0.5 Dry 2 PhL ADL M27
2 Plan Apochromat 10x 0.75 Dry 0.5 Ph1   M27
3 Plan Apochromat 20x 0.75 Dry 0.4 Ph2 ADL M27
4 Plan Apochromat 40x 0.95 Dry 0.2 DIC I   M27

Fluorescent Filter Sets:

Position Name Excitation Dichroic Emission Suitable Dyes
1 DAPI - 5060C 377/50 409LP 447/60 DAPI, Hoechst
2 CFP - 2432C 438/24 458LP 483/32 CFP, Cerulean
3 GFP-3000B 488/10 505LP 530/60 GFP, A488
4 mCherry LP 560/20 580LP 585LP mCherry, Cy3
5   - - -  
6   - - -  

Computer:

Dell PC - 3GHz Xeon Processor - 8GB RAM - 256GB nVidia Quadro GPU

1TB Raid Array

30" LCD Monitor

Software: 

Pathway

Accessories:

Incubation chamber with CO2 and Temperature control

FLIM/FRET

Current Status:  Fully Operational


Resource Links:


Room 2.138 - Olympus IX71 - Inverted Microscope Stand with Intensified CCD camera

Inverted widefield microscope with Mercury and LED lightsources and CCD camera. Suited for imaging fixed samples on slides, samples with low fluorescence and live imaging.

Features Include:

  • Manual X-Y-Z stage
  • CO2 and temperature incubation for live cells and tissue
  • Tiled imaging
  • Multi-position imaging

Transmitted Light100W Halogen Lamp

Reflected Light:  Olympus Mercury White Lightsource, Lambert LED Lightsource

Objectives:

Position Objective Magnification N.A. Immersion W.D. (mm) Type Type Thread
1 Plan Apochromat 4x 0.5 Dry 2 PhL ADL M27
2 Plan Apochromat 10x 0.75 Dry 0.5 Ph1   M27
3 Plan Apochromat 20x 0.75 Dry 0.4 Ph2 ADL M27
4 Plan Apochromat 40x 0.95 Dry 0.2 DIC I   M27

Fluorescent Filter Sets:

Position Name Excitation Dichroic Emission Suitable Dyes
1 DAPI - 5060C 377/50 409LP 447/60 DAPI, Hoechst
2 CFP - 2432C 438/24 458LP 483/32 CFP, Cerulean
3 GFP-3000B 488/10 505LP 530/60 GFP, A488
4 mCherry LP 560/20 580LP 585LP mCherry, Cy3
5   - - -  
6   - - -  

Computer:

Dell PC - 3GHz Xeon Processor - 8GB RAM - 256GB nVidia Quadro GPU

1TB Raid Array

Dual 27" LCD Monitors

Software: 

Lambert Intruments

Accessories:

Incubation chamber with CO2 and Temperature control

OPT

Current Status:  Fully Operational


Resource Links:


OPT

Room 6.025d - Custom Microscope Stand with Photometrics Coolsnap HQ2 CCD camera

Custom widefield microscope with Whitelight Mercury lightsource and CCD camera. Suited for imaging large fixed samples in 3D.

Features Include:

  • Fully motorised X-Y-Z stage

Transmitted Light100W LED Lamp

Reflected Light:  Exfo Xacte 200W Mercury White Lightsource

Objectives:

Position Objective Magnification N.A. Immersion W.D. (mm) Type Type Thread
1 Plan Apochromat 0.18x 0.04 Dry 50      
2 Plan Apochromat 0.5x 0.1 Dry 45      
3 Plan Apochromat 1x 0.2 Dry 40      

Fluorescent Filter Sets:

Position Name Excitation Dichroic Emission Suitable Dyes
1 DAPI - 5060C 377/50 409LP 447/60 DAPI, Hoechst
2 CFP - 2432C 438/24 458LP 483/32 CFP, Cerulean
3 GFP-3000B 488/10 505LP 530/60 GFP, A488
4 mCherry LP 560/20 580LP 585LP mCherry, Cy3
5   - - -  
6   - - -  

Computer:

Dell PC - 3GHz Xeon Processor - 8GB RAM - 256GB nVidia Quadro GPU

1TB Raid Array

30" LCD Monitor

Software: 

OPTiscan

Stereo 1 - Olympus SZX12

Stereo 1


Current Status:  Fully Operational


Resource Links:


Room 2.136 - Olympus SZX12 Microscope Stand with Olympus DP70 CCD camera

Stereo widefield microscope with Halogen Ring and Bifurcated lightsources  and CCD camera. Suited for imaging fixed samples and live imaging.

Features Include:

  • Manual Z Focus
  • Bifurcated Lightsource
  • Ring Lightsource

Transmitted Light100W Halogen Lamp

Objectives:

Position Objective Magnification N.A. Immersion W.D. (mm) Type Type Thread
1 Plan Apochromat 1-12x 0.2 Dry 85      

Computer:

Dell PC - 3GHz Xeon Processor - 8GB RAM - 256GB nVidia Quadro GPU

1TB HDD

30" LCD Monitor

Software: 

DP Capture

Stereo 2 - Nikon SMZ1500

Current Status:  Fully Operational


Resource Links:


Room 2.136 - Nikon SMZ-1500 Stereo Microscope Stand with Photometrics Coolsnap ES CCD camera

Stereo widefield microscope with 100W Mercury lightsource and CMOS camera. Suited for imaging fixed samples, samples with low fluorescence and live imaging.

Features Include:

  • Motorised Z Drive

Transmitted Light:  Nikon 100W Halogen Lamp

Reflected Light:  Nikon Intensilight 100W Mercury White Lightsource

Objectives:

Position Objective Magnification N.A. Immersion W.D. (mm) Type Type Thread
1 Plan Apochromat 0.5x 0.1 Dry 150      
2 Plan Apochromat 1x 0.2 Dry 100      
3 Plan Apochromat 2x 0.4 Dry 50      

Fluorescent Filter Sets:

Position Name Excitation Dichroic Emission Suitable Dyes
1 DAPI - 5060C 377/50 409LP 447/60 DAPI, Hoechst
2 CFP - 2432C 438/24 458LP 483/32 CFP, Cerulean
3 GFP-3000B 488/10 505LP 530/60 GFP, A488

Computer:

Dell PC - 3GHz Xeon Processor - 32GB RAM - 1GB nVidia Quadro GPU

1TB Raid Array

30" LCD Monitor

Software: 

NIS Elements 4.3

Stereo 3 - Nikokn SMZ1500

Current Status:  Fully Operational


Resource Links:


Room 2.136 - Nikon SMZ-1500 Stereo Microscope Stand with DXM1200 CCD camera

Stereo widefield microscope with 100W Mercury lightsource and CMOS camera. Suited for imaging fixed samples, samples with low fluorescence and live imaging.

Transmitted Light:  Nikon 100W Halogen Lamp

Reflected Light:  Nikon Intensilight 100W Mercury White Lightsource

Objectives:

Position Objective Magnification N.A. Immersion W.D. (mm) Type Type Thread
1 Plan Apochromat 0.5x 0.1 Dry 150      
2 Plan Apochromat 1x 0.2 Dry 100      
3 Plan Apochromat 2x 0.4 Dry 50      

Fluorescent Filter Sets:

Position Name Excitation Dichroic Emission Suitable Dyes
1 DAPI - 5060C 377/50 409LP 447/60 DAPI, Hoechst
2 CFP - 2432C 438/24 458LP 483/32 CFP, Cerulean
3 GFP-3000B 488/10 505LP 530/60 GFP, A488

Computer:

Dell PC - 3GHz Xeon Processor - 32GB RAM - 1GB nVidia Quadro GPU

1TB Raid Array

30" LCD Monitor

Software: 

NIS Elements 4.3

The Imaging facility currently has 4x dedicated, physical workstation computers as well as a number of virtualised machines available for image processing and visualisation of your microscopy data.

 Analysis virtual machines are high-powered, graphics accelerated computers available to all users of the imaging facility to access, either onsite at the Queensland Bioscience Precinct, or remotely via VPN. These machines are installed with multiple different software packages including all of the relevant vender software (Zen, LAS X, NIS Elements Viewer) as well as advanced visualisation and analysis tools including Imaris 9, and FIJI/ImageJ.

These virtual machines are Big Data Ready! This means they have a large allocation of RAM (>100gb), the latest NVIDIA GPUs (GTX1080), high-speed network connections, large dedicated scratch workspace (>10tb) and the latest visualisation software. For large datasets (Spinning Disc Confocal, Lattice Lightsheet Microscope, Nikon deconvolution) we recommend Imaris 9 for visualisation and quantification.

Access to these machines within IMB, requires a VNC client (Turbo VNC, TigerVNC, VNC Viewer), while access from outside of IMB will also require Cisco Anyconnect software in addition to a VNC viewer. Bookings for these machines are available via PPMS.imb.uq.edu.au.