Specifications

Microscope Specifications

The Microscopy Facility provides advanced imaging tools and computational resources for researchers to generate detailed views of the systems and processes occurring in the brain.

Finding the right microscope for your research is paramount, the microscopy team can assist with choosing the right equipment for your needs or you can view our capabilities for the following state-of-art microscopes.

Zeiss LS M 780

Confocal laser scanning microscope used for optical sectioning, fixed tissue

The Zeiss Axio observer LSM 780 is an upright confocal microscope that can be used to image fixed cells and tissues. It is fitted with a piezo stage and can be used with a slide holder (two slides) or a universal stage insert.

A unique feature of this instrument is the simultaneous imaging of up to ten channels with the GaAsP detector array. This instrument can be fitted with long working distance 20x NA1.0 dipping lens to image cleared brain samples (can be used for SCALEVIEW as well as CLARITY cleared samples).

Image of microscope Zeiss LSM 780
Image of microscope Zeiss LSM 780

Applications

  • z-stack
  • Tile scan
  • Multi positions
  • Spectral unmixing
  • Online finger printing
  • Reflection imaging
  • DIC

Light sources

  • Metal halide fluorescent lamp
  • Diode laser- 405 nm
  • Argo laser- 458, 488 and 514 nm
  • Diode pumped solid state laser- 561 nm
  • HeNe laser – 594 and 633 nm

Objective details

Objective N.A Immersion media Working distance (mm)
PL-APO 10 (DIC) 0.45 Air 2.000
PL-APO 10 (DIC) 0.45 Air 2.000
PL-APO 10 (DIC) 0.45 Air 2.000
PL-APO 10 (DIC) 0.45 Air 2.000
PL-APO 10 (DIC) 0.45 Air 2.000

Detectors

  • 3 fluorescence PMTs,
  • 2 HyD GaAsP
  • 1 transmitted light

Software

  • Las X Navigator

Leica TCS SP8

Confocal laser scanning microscope used for optical sectioning, live and fixed cell or tissue

The Leica SP8 confocal microscope is an inverted microscope that can be used to image live and fixed cells as well as tissues. This system can be used with an 8 kHz resonant scanner to image dynamic cellular processes. It is fitted with an incubator for temperature, humidity and CO2 control.

Features include fast imaging of up to five channels simultaneously, high flexibility with acousto-optic beam splitter (AOBS), excellent imaging of dim staining using sensitive HyD detectors with outstanding quantum efficiency.

Microscope_Leica TCS SP8

Applications

  • DIC
  • FRET/FRAP wizard
  • Live cell imaging
  • Multi positions
  • Tile scan
  • Time series
  • Z-stack

Light sources

  • Metal halide fluorescent lamp
  • Diode laser- 405 nm
  • Argo laser- 458, 476, 488, 496 and 514 nm
  • Diode pumped solid state laser- 561 nm
  • HeNe laser – 633 nm

Objective details

Objective N.A Immersion media Working distance (mm)
HC PL-APO 10 (DIC)  0.40 Air 2.200
HC PL-APO 20 (DIC)  0.75 Air 1.150
HC PL-APO 40 (DIC)  1.30 Oil 0.100
HCX PL-FL 40 (corr)  0.60 Air 3.300-1.900
HC PL-APO 63 (DIC)  1.40 Oil 0.100
HC PL APO 63  (corr) 
1.30 Glycerol 0.280

Detectors

  • 3 fluorescence PMTs,
  • 2 HyD GaAsP
  • 1 transmitted light

Software

  • Las X Navigator

Zeiss Axio Imager M2 with Apotome

The Zeiss Axio Imager is an upright microscope that can be used to image brightfield and fluorescent samples on slides. This instrument also has an ApoTome for optical sectioning of fluorescent samples.

Microscope_Zeiss-Axio-Imager-M2-with-Apotome
Zeiss Axio Imager, installed 2017

Applications

  • Brightfield imaging
  • Fixed tissue imaging
  • Fluorescent imaging
  • Neuron tracing
  • Optical sectioning with ApoTome
  • Stereology
  • Tile scan
  • Z-stack

Light sources

  • Epi-fluorescent Colibri 7.7 LED illumination
  • Brightfield LED illumination

Fluorescent filter sets

Filter cubes Excitation Dichromatic mirror Emission filter
Filter set 90 HE LED (E) suitable for fluorescent dyes like DAPI, FITC, TRITC and Cy5 385, 475, 555 and 630 nm
Filter set 96 HE BFP shift free (E) EX BP 390/40 420 EM BP 450/40
38 HE eGFP shift free (E) EX BP 470/40 495 EM BP 525/50
Filter set 43 HE Cy 3 shift free (E) BP 550/25 570 EM BP 605/70
Filter set 50 Cy 5 shift free (E) BP 640/30 660 EM BP 690/50

 

Objective details

Objective NA Immersion media Working distance (mm)
EC PL-Neofluar 2.5 0.085 Air 8.80
PL-APO 10 0.45 Air 2.10
PL-APO 20 0.80 Air 0.55
EC PL-Neofluar 40 1.30 Oil 0.21
PL-APO 63 1.40 Oil 0.19
PL-APO 100 1.40 Oil 0.17

Cameras

Lumina HR and Hamamatsu Orca-Flash 4 CMOS cameras

Stage

Motorised linear encoded XY and Z stage

Software

LuCam and HCImaging for basic image acquisition

Stereo Investigator

Neurolucida 360

Zeiss LSM 900

Confocal laser scanning microscope used for optical sectioning and super resolution image acquisition, fixed tissue.

The Zeiss Axio Observer 7 LSM 900 is an upright confocal microscope that can be used to image fixed cells and tissues. The system is fitted with a multi-immersion 25x/0.8NA objective and monochrome AxioCam 712 for fluorescent imaging too.

The unique feature of this system is the Airyscan 2, a fibre-coupled 32 array channel GaAsp detector which can capture super resolution images.

Zeiss LSM 900
Zeiss LSM 900, installed 2022

Applications

  • Fixed tissue imaging
  • Fluorescent imaging
  • Spectral imaging
  • Super resolution imaging
  • Tile scan
  • Transmitted light imaging
  • Z-stack

Light Sources

  • Colibri 7
  • Transmitted LED
  • Main Beam Splitter (405, 488, 561, 640nm)

Filter sets

Filter cube Excitation (nm) Dichromatic mirror (nm) Emission filter (nm)
90 HE LED 382 QBS 405 QBP 245/30
475 QBS 493 QBP 514/30
555 QBS 575 QBP 592/25
630 QBS 653 QBP 709/100
91 HE LED 430 TBS 450 TBP 467/24
511 TBS 538 TBP 555/25
590 TBS 610 TBP 687/145

Objective details

Objective NA Immersion media Working distance (mm)
EC PL Neofluar 5 0.16 Air 18.50
PL-APO 10 0.45 Air 2.0
PL-APO 20 0.8 Air 0.55
PL-APO 25 0.8 Water, silicone, oil, glycerol 0.57
PL APO-40 1.3 Oil 0.2
PL-APO 63 1.4 Oil 0.14

Detectors

Fibre-coupled 32 channel GaAsp array Airyscan 2 detector
2x GaAsp detectors
ESID transmitted light detector
Axiocam 712 mono (3.45 x 3.45µm pixels)

Software

Zen Blue

Leica Thunder

Fluorescence microscope for high throughput optical sectioning of live and fixed cells or tissue.

The Leica Thunder is an inverted fluorescence microscope that can be used to image live and fixed cells and tissues. The system boasts high speed image acquisition capabilities which is useful for high throughput experiments. Interoperability with the Leica SP8 enables seamless transition of workflows from one system to another.

Features include closed loop focusing, environmental chamber, instant computational clearing and deconvolution to generate clear and crisp images.

Leica Thunder Imager
Leica Thunder Imager, installed 2021

Applications

  • High throughput imaging
  • Live cell imaging
  • Multi positions
  • Tile scan
  • Time series
  • Z-stack

Light Source

  • Epifluorescent LED 8 (395,438,475,511,555,575,635,730nm)

Fluorescent filter set

Filter set Excitation Dichromatic mirror Emission filter
DTF51011, size P 391/32 415 440/40
479/33 500 510/40
554/24 572 590/50
638/31 660 700/75
CYR71010 436/28 459 473/22
506/21 523 539/24
578/24 598 641/78
730/40 763 810/80
100% transmission

 

Objective details

Objective NA Immersion media Working distance (mm)
N PL 5 0.12 Dry 14
HC PL Fluotar 10 0.30 Dry 11
HC PL FL L 20 0.40 Dry 7.5-6.2
HC PL APO 20 0.80 Dry 0.40
HC Fluotar 25 0.95 Water 2.4
HC PL APO 63 (corr) 1.4-0.60 Oil 0.14

 

Camera

Leica K5 sCMOS camera (2048 x 2048 resolution, 6.5 x 6.5 µm pixel)

Stage

Motorised linear encoded XY and Z stage

Software

LAS X 3D

Olympus BX51

The Olympus BX51 is an upright microscope that can be used to image brightfield and fluorescent samples on slides.

Olympus BX51
Olympus BX51

Applications

  • Fluorescent imaging
  • Stereology
  • Tile scan
  • Transmitted light imaging

Light sources

  • 12V/ 100W HLX Xenophot 64625 Halogen lamp (BF)
  • HBO 100W Hg short arc lamp (Fluorescence)

Fluorescent filter sets

Filter cubes Excitation Dichromatic mirror Emission filter
UMWU2(UV) UV wide (BP 330-385) 400 BA420
UMNIBA2 (Blue) Blue narrow (BP 470-490) 505 Bandpass (BA 510-550)
UMWIB2 (Blue) Blue wide (BP 460-490) 505 Interference (BA510IF)
UMWIG2 Green wide (BP520-550) 565 Interference (BA580IF)
U-MNG2 Green narrow (BP530-550) 570 Standard BA590

 

Objective details

Objective NA Immersion media Working distance (mm)
PL 2 0.05 Air 5.80
UPLSAPO 10 0.40 Air 3.10
UPLSAPO 20 0.7 Air 0.60
UPLSAPO 40 0.75 Air 0.51
UPLSAPO 60 1.35 (DM Ph4) Oil 0.15
UPLSAPO 100 1.40 Oil 0.20

 

 

Cameras

Q Imaging and Hamamatsu Orca R2 cameras

Stage

Motorised LudL XY stage

Software

QCapture and HCImaging for basic image acquisition
Stereo Investigator

Nikon-Crest Optics Spinning Disk Confocal

An inverted microscope with Crest V3 light spinning disk and DeepSIM for both high-resolution and tissue imaging.

Simultaneous dual-channel camera acquisition with up to 25mm view.

Nikon Crest Spinning Disk with DeepSIM
Nikon Crest Spinning Disk with DeepSIM

Applications

  • Confocal imaging
  • Fluorescent imaging
  • Imaging with large field of view
  • Super resolution
  • Tile scan
  • Transmitted light imaging
  • Z-stack

Light sources

  • D-Ledi LED system (385, 475, 550, and 621nm)
  • Solid state lasers 405, 488, 555, 640 and 730nm
Filter cube Excitation Emission filter (nm)
5-way (ZET 405/488/555/640/730 r25mm) 405

488,

555

640

730

440/60

520/40

590/50

680/50

825/150

ET 440 40
ET 525 50
ET 600 50
ET 667 60
ET 811 80
4-way(ZET405/488/555/640) 405

405

488

555

640

440/60

520/40

590/50

720/70

Splitter 565 long pass

 

Objective details

Objective NA Immersion media Working distance (mm)
PL-APO 4 0.2 Air 20
PL-APO 10 0.45 Air 4
PL-APO 20 0.8 Air 8
PL-APO 25 1.05 Silicone 0.55
PL-APO 40 1.25 Silicone 0.55
PL-APO 60 1.42 Oil 0.15
PL-APO 100 1.45 Oil 0.13

 

Cameras

2 x Photometrics Kinetix CMOS (large field of view imaging, 6.5 x 6.5µm pixel)

Stage

Motorised XY and Z stage and piezo z-drive

Software

NIS Elements

Precision Analysis workstation

Image analysis workstation used for 3D analysis and quantification consisting of a PC with Imaris, FIJI, LASX Core Offline and ZEN Blue lite.

Imaris Core Facilities. Enable 3D/4D visualisation and analyses including cell counts, volume analysis and colocalisation of confocal data. Generate 3D visuals to add to presentations. Interface for customisation with Matlab, Java or Python.

FIJI is an open-source processing package used for image analysis.

Leica’s LASX Core Offline software enables manipulation and analysis of images captured on Leica systems.

Zeiss’s Zen Blue Desktop with deconvolution toolkit enables users to visualise and post-process images captured on Zeiss hardware.

PC: Windows 10, 1x Intel Xeon Gold 6246R 3.4GHz (4.1GHz Turbo, 16C), 256GB 8X32GB DDR4 3200MHz RDIMM ECC Memory, M.2 512GB PCIe NVMe Class 50 SSD (Internal PCI card), Additional storage 2 x 3.5″ 1TB 7200rpm SATA Hard Drive (configured in RAID 1 via PERC PCIe controller), NVIDIA Quadro RTX4000 8GB, iDRAC Enterprise

Offline image analysis workstation

Image analysis workstation used for 3D reconstruction, quantification and deconvolution consisting of a PC with Stereo Investigator desktop version, Neurolucida 360 lite, Huygens essential, Zen Blue and FIJI.

The desktop version of Stereo Investigator can be used to perform stereology at the PC using image stacks and virtual image slices.

  • Neurolucida 360 lite is used to reconstruct neuronal structures such as dendrites and axons.
  • Huygens essential can be used to post-process and deconvolve images.
  • The Zen Blue lite software allows for processing and analysis of images captured on the Zeiss confocals.
  • FIJI is an open-source processing package used for image analysis.

PC: 64-bit PC workstation. Intel® Quad Core Xeon Processor ES 1630 v4 3.7GHz, 10MB cache, 64GB 2400MHz. DDR4 RDIMM memory, 2 x 512GB Solid State Drives in RAID 1 configuration (total 512GB storage) and 8GB GDDR5 video card. Dual monitors.