Technical Data for Microscope Core Facility

Facility Head:

Dr Anand JEYASEKHARAN,

CSI Singapore
Email: csiadj[at]nus.edu.sg

Nikon A1R Confocal

Nikon A1R Confocal – 13 South confocal room

nikon a1r

The Nikon A1R is a modular confocal system consisting of a separate scan head, standard 4 PMT detector module plus an additional PMT for pseudo-DIC imaging, control module, laser module, and spectral detector module. The A1R has a standard high-resolution confocal mode (up to 4096 x 4096 pixels) as well as a high speed resonant mode capable of scanning 230 frames per sec at 512 x 64 pixels. In addition to laser-based, confocal image acquisition, this Nikon platform also utilizes a high-end digital camera for non-confocal image acquisition.

Features:

  • Fully motorized Nikon Eclipse Ti Inverted Trinocular Microscope with perfect focus system
  • Fluorescent Illumination: C-HGFI Intensilight 130W mercury lamp
  • Resonant (fast scanning) and non-resonant galvano (conventional scanning) scanning mirrors
  • Ideal for live-cell photo-activation and photo-bleaching studies where resonant scanning can be used to capture images at high-speed and non-resonant scanning can be used to target a region of interest for photo-activation
  • Multispectral imaging can be carried out on the 32 PMT detector and images can be spectrally unmixed to provide accurate quantitative data free from autofluorescence
  • The system is run through Nikon’s versatile Elements software package and incorporates wizards to perform common imaging tasks such as FRAP, FRET and colocalisation as well as data quantification

Filter sets:

Filter set 1 (DAPI, Hoechst, AlexaFluor 405, Pacific Blue, Cascade Blue, Coumarin) Filter set 2 (FITC, GFP, eCFP) Filter set 3 (TRITC, AlexaFluors 546, 551, 568, Cy3, DiI, DsRed, mCherry, PE, PI, RFP, tdTomato,) Filter set 4 (Cy5, Alexafluors 633, 647, To-PRO-3)
Ex/Em 330 – 380 nm / 420 nm 465 – 495 nm / 515 – 555 nm 540/25 nm  / 605/55 nm 590-650 nm / 663-738 nm
Beamsplitter 400 nm 505 nm 565 nm 660 nm

 

Objectives:

  • Plan Apo 10X/0.45
  • Plan Apo VC 20X/0.75 DIC N2
  • Plan Apo 40X/0.95
  • Plan Apo VC 60X/1.40 Oil DIC N2
  • Plan Apo VC 100X/1.40 Oil DIC N2

Laser Module (Class 3b):

  • L1 CVI Melles Griot 50mW 640nm for Cy5
  • L2 Coherent Diode 100mW 405nm for DAPI
  • L3 CVI Melles Griot Argon-Ion (457nm, 477nm, 488nm, 514nm) for CFP, GFP, FITC, YFP
  • L4 Coherent Diode 20mW 561nm for TRITC

Detector:

  • 4 PMT Standard Fluorescence Detector
  • 32 PMT with 2.5nm, 5nm and 10nm grating for multispectral imaging
  • Nikon DSQi1 monochrome CCD for non-confocal image capture

Software:

  • Microsoft Windows 7 Pro with Nikon NI-Elements (Advanced Research)

Applications:

  • Z-stack: generation of a Z-series that dissect through the specimen to get 3D and 4D images
  • Co-localization of proteins: 4 color imaging to detect the distribution of various fluorescently-tagged proteins using the standard detector
  • Multispectral imaging and spectral unmixing to separate emission based on spectral properties rather than through band-pass filtering. Spectral unmixing allows users to very specifically eliminate tissue autofluorescence without compromising the intensity of the actual fluorescence staining.
  • Time lapse: observation and record sample response under certain treatment. Fast scanning mode to study movement cellular dynamics over time
  • Dynamic study in live cells, i.e. Fluorescent Resonant Energy Transfer (FRET), Fluorescent Recovery after Photo-bleaching (FRAP) and Fluorescent Loss in Photo-bleaching (FLIP), etc

Nikon C1 Confocal

Nikon C1 Confocal – 13 South confocal room

nikon c1

The Eclipse C1 Plus is a modular confocal imaging system that gives you the highest-quality digital images with an ultra-compact and lightweight design. The improved scan head optics of the C1 Plus boost optical performance to 400nm and its bi-directional scanner provides faster image acquisition. The system also includes support for X and Y scan axes rotation and new laser options for improved control over laser illumination intensity.

Features:

  • Motorized Nikon TE2000S Inverted Trinocular Microscope
  • The microscope is fully-enclosed in a heated environmental chamber and has the ability to set, maintain and monitor temperature, humidity, CO2 and O2 levels as imaging conditions dictate
  • Fluorescent illumination: C-HGFI Intensilight 130 W mercury lamp

Filter Sets:

Filter set 1 (DAPI) Filter set 2 (CFPHQ) Filter set 3 (FITC) Filter set 4 (Cy3) Filter set 5 (YFPHQ)
Ex/Em 340 – 380 nm / 435 – 485 nm 420 – 445 nm / 460 – 510 nm 465 – 495 nm  / 515 – 555 nm 512 – 552 nm / 565 – 615 nm 490 – 500 nm / 520 – 560 nm
Beamsplitter 400 nm 450 nm 505 nm 512 nm 510 nm

 

Objectives:

  • Nikon 10X / 0.45 Plan Fluor
  • Nikon 20X / 0.60 Plan Fluor
  • Nikon 60X / 1.40 Oil Plan Apo DC DIC
  • Nikon 100X / 1.40 Oil Plan Apo VS

Laser Module (Class 3b):

  • L2 Coherent Diode 100mW 405nm for DAPI
  • L3 CVI Melles Griot Argon-Ion (457nm, 477nm, 488nm, 514nm) for CFP, GFP, FITC, YFP
  • L4 G-HeNe 543nm for TRITC, Cy3, DsRed

Detector:

  • 3 PMT
  • Nikon DSQi1 monochrome CCD for non-confocal image capture

Software:

  • Nikon NIS Elements AR
  • Nikon EZ-C1

Applications:

  • Z-stack: generation of a Z-series that dissect through the specimen to get 3D and 4D imaging
  • Co-localization of proteins: multi-color imaging to detect the distribution of various fluorescently-tagged proteins
  • Time lapse: observation and record sample response under certain treatment
  • Dynamic study in live cells, i.e. Fluorescent Resonant Energy Transfer (FRET), Fluorescent Recovery after Photo-bleaching (FRAP) and Fluorescent Loss in Photo-bleaching (FLIP), etc
  • CO2 incubator with temperature control and heated stage for live cell imaging

Zeiss Axio Z1 with Cell Observer

Zeiss Axio Z1 with Cell Observer – 13 North Live Imaging room

zeiss axio z1

Features:

  • Motorized inverted brightfield and fluorescence trinocular microscope
  • The microscope is fully-enclosed in a heated environmental chamber and has the ability to set, maintain and monitor temperature, humidity, CO2 and O2 levels as imaging conditions dictate
  • Zeiss Apotome 2 for highly resolved and enhanced z-stack image capture through the use of structured illumination to reduce light from out of focus planes
  • Colibri 2 LED lamps allows adjustment of each illumination intensity depending on the sensitivity of the sample. The narrow-band illumination reduces cross-stimulation, increasing the sensitivity of your images.

 

Filter Sets:

Filter set 62 HE B/G/HR (DAPI, GFP, HcRed) Filter set 43 (Cy3, DsRed) Filter set 46 (YFP) Filter set 47 (
CFP)
Ex/Em EX BP 370/40BP 474/28BP 585/35EM DBP 425/46+527/54+LP 615 EX  BP 545/25EM BP 605/70 EX BP 500/20EM  BP 535/30 EX BP 436/20EM  BP 480/40
Beamsplitter BS TFT 395+495+610 FT 570 FT 515 FT 455

 

Objectives:

  • EC Plan Neofluar 10X/0.30 Ph1
  • LD Plan Neofluar 20X/0.40 Ph2 M27
  • LD Plan Neofluar 40X/0.60 Korr Ph2 M27
  • Plan-Apochromat 63X/1.40 Oil DIC M27

Fluorescence Illumination:

  • Colibri 2 LED illumination

o   365 nm

o   470 nm

o   555 nm

o   590 nm

  • HXP 120C metal halide lamp

Camera:

  • Zeiss Axiocam MRm monochrome camera

Software:

  • Zeiss Axiovision 4.6

Applications:

  • Co-localization of proteins: multi-color imaging to detect the distribution of various fluorescently-tagged proteins
  • Time lapse: observation and record sample response under certain treatment
  • 3D optical slice image capture using Apotome 2 structured illumination
  • Dynamic study in live cells, i.e. Fluorescent Resonant Energy Transfer (FRET), Fluorescent Recovery after Photo-bleaching (FRAP) and Fluorescent Loss in Photo-bleaching (FLIP), etc
  • CO2 incubator with temperature control and heated stage for live cell imaging
  • Colibri 2 LED light source for minimal cell phototoxicity and photobleaching during long duration fluorescence live cell imaging

Zeiss Axio Imager M2

Zeiss Axio Imager M2 – 11 North microscope room

zeiss axio imager m2

Features:

  • Motorized upright brightfield and fluorescence trinocular microscope
  • Touch screen for easy control over motorized components
  • Automated tiling function for large sample imaging
  • Fast, high resolution cooled CCD camera for quantitative fluorescence microscopy

Filter Sets:

Filter set 02 (DAPI) Filter set 03 (FITC) Filter set 04 (Cy3) Filter set 05 (Cy5) Filter set 06 (CFP)
Ex/Em Ex BP 365Em LP 397 Ex BP 450 – 490Em BP 515 – 565 Ex BP 546Em LP 590 Ex BP 640/30Em BP 690/50 Ex BP 436/20Em BP 480/40
Beamsplitter FT 395 FT 510 FT 580 FT 660 455

 

Objectives:

  • Zeiss Plan-NEOFLUAR 5X / 0.16 Ph1
  • Zeiss EC Plan NEOFLUAR 10X / 0.3 Ph1
  • Zeiss EC Plan NEOFLUAR 20X / 0.5 Ph2
  • Zeiss EC Plan NEOFLUAR 40X / 0.75 Ph2
  • Zeiss EC Plan NEOFLUAR 63X / 1.25 Oil

Fluorescence Illumination: X-Cite Series 120 Q

Camera: Photometrics CoolSnap HQ2 monochrome CCD camera with 1392 x 1040 imaging array (6.45 x 6.45-μm pixels)

Software: Microsoft Windows 7 Pro with Zeiss ZenBlue (Dell Optiplex 3010 with Intel Core i5, Win 7 and 1TB HDD)

Applications:

  • Quantitative fluorescence imaging for fixed or live cells
  • High resolution bright field imaging with phase contrast for live cell morphology study, and/or HE and immunochemical stained slides
  • Multi dimension fluorescence imaging: multi-location, time lapse, multi-channel

Zeiss Axiovert A1

Zeiss Axiovert A1 – 11 North microscope room

Zeiss Axiovert A1

Features:

  • Inverted manual brightfield and fluorescent trinocular microscope for high resolution brightfield and fluorescence imaging
  • Phase contrast can be obtained with the 5X, 10X, 20X and 40X objectives
  • High resolution and sensitive cooled monochrome CCD

 

Filter Sets:

Filter set 02 (DAPI) Filter set 03 (FITC) Filter set 04 (Rhodamine) Filter set 05 (EGFP)
Ex/Em BP 365 / LP 397 BP 450 – 490  / BP 515 – 565 BP 546 / LP 590 BP 470 / BP 525
Beamsplitter FT 395 FT 510 FT 580 FT 495

 

Objectives:

  • Zeiss N-Achroplan 5X / 0.15 Ph1
  • Zeiss N-Achroplan 10X / 0.25 Ph1
  • Zeiss LD Plan NEOFLUAR 20X / 0.4 Ph2 Korr
  • Zeiss LD Plan NEOFLUAR 40X / 0.6 Ph2 Korr

Fluorescence Illumination: X-Cite Series 120 Q

Camera: Photometrics CoolSnap HQ2 monochrome CCD camera with 1392 x 1040 imaging array (6.45 x 6.45-μm pixels)

Software: Microsoft Windows 7 Pro with ZenBlue (Dell Optiplex 3010 with Intel Core i5, Win 7 and 1TB HDD)

Applications:

  • Long Working Distance (LD) objectives ideal for fluorescence imaging for fixed or live cells in multi-well plates and petri dishes
  • High resolution bright field imaging for live cell morphology study, and/or HE and immunochemical stained slides

Zeiss Axioplan 2

Zeiss Axioplan 2 – 12 North microscope room

Zeiss Axioplan 2

Features:

  • Upright motorized brightfield and fluorescence trinocular microscope
  • High resolution brightfield, phase contrast and DIC illumination
  • Easy to use with predefined user settings for brightfield, phase contrast, DIC and fluorescence imaging

 

 

Filter Sets:

Filter set 02 (DAPI) Filter set 03 (FITC) Filter set 04 (Rhodamine) Filter set 05 (EGFP)
Ex/Em BP 365 / LP 397 BP 450 – 490  / BP 515 – 565 BP 546 / LP 590 BP 470 / BP 525
Beamsplitter FT 395 FT 510 FT 580 FT 495

 

Objectives:

  • Zeiss Plan NEOFLUOR 5X / 0.15
  • Zeiss Plan NEOFLUOR 10X / 0.30 Ph1
  • Zeiss Plan NEOFLUOR 20X / 0.50 Ph2
  • Zeiss Plan NEOFLUOR 40X / 0.75
  • Zeiss Plan NEOFLUOR 100X / 1.30 Oil Ph3

Fluorescence Illumination:

  • HBO 103 12V 100W mercury arc lamp

Camera: Zeiss AxioCam HrC (color image capture at 3900 x 3090 pixel resolution)

Software: Microsoft Windows XP with Zeiss AxioVision 4.6.3

Applications:

  • Fluorescence imaging for fixed or live cells
  • High resolution bright field imaging for live cell morphology study, and/or HE and immunochemical stained slides
  • Automated multidimensional and multicolour imaging of samples
  • High magnification objective (100X) can be used to image bacterial cells

Olympus IX71

Olympus IX71 – 12 North microscope room

Olympus IX71

Features:

  • Manual inverted brightfield and fluorescence trinocular microscope useful for imaging samples in multi well plates
  • Phase contrast can be obtained with the 10X, 20X and 40X objectives
  • Useful for imaging of bacterial cells that require high (100X) magnification
  • Correction rings on objectives to

Filter Sets:

Filter set WU (DAPI) Filter set WIBA (FITC, GFP) Filter set WIGA ( TRITC)
Ex/Em 360 – 370nm / 420nm 460 – 490 nm / 515 nm 515 – 550 nm  / 600 – 640 nm
Beamsplitter 400 nm 505 nm 580 nm

 

Objectives:

  • UPlan FL N 4X/0.13 PhL
  • UPlan FL N 10X/0.30 Ph1
  • LUC UPlan FL 20X/0.45 Ph1
  • LUC UPlan FL 40X/0.60 Ph2
  • UPlan FL N 100X/1.30 Oil

Fluorescence Illumination:

  • Olympus HBO103W/2 mercury arc lamp

Camera:

  • Olympus DP71 cooled colour CCD (12.5MP capture at 4080×3072 resolution)

Software: Microsoft Windows Vista with DP Controller

Applications:

  • Routine imaging of samples in brightfield, phase contrast or fluorescence illumination
  • Fluorescence imaging of fixed or live cells on glass slides, multi-well plates or petri dishes
  • High magnification objective can be used to image bacterial cells

Olympus SZX12

Olympus SZX12 – 12 North microscope room

Olympus SZX12

Features:

  • High performance zoom trinocular stereomicroscope for imaging large samples (eg mouse embryo, zebrafish) in brightfield or fluorescence illumination
  • Long working distance, wide zoom range, excellent image clarity and easy operation to allow a wide range of application

Filter Sets:

Filter set G Filter set GFP
Ex/Em 460 – 560nm / 590nm 460 – 490 nm / 510 nm

 

Objectives:

  • 0.5X and 1X

Fluorescence Illumination:

  • Olympus HBO103W/2 mercury arc lamp

Camera:

  • Olympus DP70 cooled colour CCD (12.5MP capture at 4080×3072 resolution)

Software:

  • Olympus DP Controller

Applications:

  • Viewing larger samples such as insects, plants, zebrafish, etc
  • Can be used with either transmitted brightfield (BF), darkfield (DF) illumination or  fluorescence excitation

Zeiss PALM LCM

Zeiss PALM LCM – 13 North histology room

Zeiss PALM LCM

Features:

  • Inverted motorized brightfield microscope (Zeiss AxioVert 200M)
  • UV 337 nm laser line for highly accurate laser capture microdissection of target samples
  • RoboMover stage for high throughput, automated dissection and capture of target samples

Objectives:

  • Plan Fluor 10X/0.5
  • LD Achroplan 40X/0.6
  • Plan NeoFluor 100X Oil/1.30

Laser Modules:

  • UV 337 nm

Detector:

  • Hitachi HV-D30 Colour Camera

Software:

  • Microsoft Windows XP with RoboSoftware version 3.2.0.11

Applications:

  • Non-contact laser microdissection of DNA, RNA and cells for easy and accurate contaminant-free sample preparation and manipulation
  • Automated, high throughput collection of pure cell cultures for downstream applications
  • Isolation and collection of individual chromosomes for analysis

Nikon Eclipse TE2000S

Nikon Eclipse TE2000S – 12 North microscope room

Nikon Eclipse TE2000S

Features:

  • Manual inverted brightfield and fluorescence microscope for routine imaging of samples in phase contrast or fluorescence modes

Filter Sets:

Filter set UV (DAPI) Filter set B (FITC, GFP) Filter set G (TRITC)
Ex/Em 330 – 380 nm / 420 nm 465 – 495 nm / 515 – 555 nm 540/25 nm  / 605/55 nm
Beamsplitter 400 nm 505 nm 565 nm

 

Objectives:

  • DL Plan Fluor 4X/0.13 PhL
  • DL Plan Fluor 10X/0.30 Ph1
  • Plan Fluor ELWD 20X/0.45
  • Plan Fluor ELWD 40X/0.60

Fluorescence Illumination:

  • Nikon 130W mercury lamp

Camera:

  • Nikon DSQi1 Cooled monochrome CCD (1.5MP 2/3-in. square pixel CCD)

Software:

  • Microsoft Windows XP with Nikon NIS Elements F

Applications:

  • Fluorescence imaging for fixed or live cells
  • High resolution bright field imaging for live cell morphology study, and/or HE and immunochemical stained slides
  • Reflected-light technique for information on texture of smooth surfaces

Nikon TS100

Nikon TS100 – 13 North live imaging room 

Nikon TS100

Features:

  • Inverted brightfield and fluorescence trinocular microscope for routine imaging of cell and tissue samples
  • TI-FM Epi-fluorescence attachment with Blue and Green filters
  • Nikon DSFi1 CCD camera attached to a standalone camera control unit DS-L2 for image capture without the use of a PC (USB storage device needed to acquire images)

Filter Sets

Filter set B (FITC, GFP) Filter set G (TRITC)
Ex/Em 450 – 490 nm / 520 nm 510 – 560 nm  / 590 nm
Beamsplitter 505 nm 575 nm

 

Objectives:

  • CFI  Plan Fluor DL 4X PhL (N.A 0.13, WD 16.4mm)
  • CFI  Plan Fluor DL 10X Ph1 (N.A 0.30, WD 16.0mm)
  • CFI  Plan Fluor DLL 20X Ph1 (N.A 0.50, WD 2.1mm)
  • CFI  Plan Fluor DLL 40X Ph2 (N.A 0.75, WD 0.72mm)

Fluorescence Illumination:

  • Nikon HG lamp C-LHGFI precentered fibre illuminator

Camera:

  • Nikon DSFi1 2/3-inch 5.24 MP colour CCD

Software:

  • Nikon DS-L2 camera controller

Applications:

  • Routine imaging of samples through brightfield, phase contrast and fluorescence imaging methods
  • ELWD condenser: N.A. 0.3 (O.D. 75mm) for imaging of cells in petri dishes or multi-well plates

190mm high stage (when the condenser is removed) allows for imaging of cell cultures at the bottom of a tall flask or testing chamber

Perkin Elmer Vectra Multispectral Imager

Perkin Elmer Vectra Multispectral Imager – 13 North histology room 

Perkin Elmer Vectra Multispectral Imager

Features:

  • Automated high-throughput slide scanning and analysis for tissue and TMA samples
  • Scanning of H&E, IHC or IF stains with the ability for multi-colour or multi-spectral imaging
  • inForm tissue finder software allows system to automatically segment regions of interest based on user specifications
  • Quantitative data can be generated and exported to industry-standard formats

Objectives:

  • Olympus Plan S Apo 4X / 0.16
  • Olympus UPlan FL N 10X / 0.30
  • Olympus UPlan S Apo 20X / 0.75
  • Olympus UPlan S Apo 40X/0.95

Fluorescence Illumination:

  • 200 W PRIOR metal halide illuminator with liquid light guide

Camera:

  • Vectra imaging module – high resolution CCD imaging sensor
  • Solid state liquid crystal (LC) wavelength tuning element for multispectral imaging (420 nm to 700 nm)

Software:

  • inForm 2.0 image analysis software

Applications:

  • Simultaneous imaging of IHC staining of different antigens in the same section
  • Multicolour staining of ER, PR, Her1 and Her2 in a single breast tissue section
  • Automatic identification and analysis of necrosis in liver tissues
  • Multicolour staining of DNA with DAPI, smooth muscle-myosin heavy chain (SM-MHC) with Cy2 and smooth muscle α-actin (SMA) with Cy3 in muscles

Zeiss Axiovert 200

Zeiss Axiovert 200 – 12 North microscope room 

Zeiss Axiovert 200 – 12 North microscope room

Features:

  • Manual inverted brightfield and fluorescence trinocular microscope for routine imaging of cells in culture dishes and multi well plates
  • Phase contrast can be obtained with the 10X, 20X and 40X objectives
  • Useful for imaging of bacterial cells that require high (100X) magnification

 

Filter Sets:

Filter set 02 (DAPI) Filter set 03 (FITC) Filter set 46 (YFP) Filter set 47 (
CFP)
Filter set 04 (Rhodamine)
Ex/Em BP 365 / LP 397 BP 450 – 490  / BP 515 – 565 Ex BP 500/20Em  BP 535/30 Ex BP 436/20Em  BP 480/40 BP 546 / LP 590
Beamsplitter FT 395 FT 510 FT 515 FT 455 FT 580

 

 

 

Objectives:

  • Zeiss A-Plan 5X/0.12 Ph0
  • Zeiss A-Plan 10X/0.25 Ph1
  • Zeiss LD A-Plan 20X/0.30 Ph1
  • Zeiss LD C-Apochromat 40X/1.1 W Corr
  • Zeiss 100X Oil

Fluorescence Illumination:

  • Zeiss HBO 100

Camera:

  • Canon PowerShot G6 with adapter tube

Software:

  • N.A

Applications:

  • Long Working Distance (LD) objectives ideal for fluorescence imaging for fixed or live cells in multi-well plates and petri dishes
  • High resolution bright field imaging for live cell morphology study, and/or HE and immunochemical stained slides

Leica DM2500 Multiview with 5 stations

Leica DM2500 Multiview with 5 stations – 12 North microscope room

Leica DM2500 Multiview with 5 stations

Features:

  • High resolution brightfield upright microscope with 5 viewing stations
  • Multiple viewing stations accommodates up to 5 stations for simultaneous viewing of brightfield illuminated samples
  • Image orientation is identical to instructor

Objectives:

  • N PLAN 2.5X/0.07
  • HI PLAN 4X/0.10
  • HI PLAN 20X/0.40
  • HI PLAN 40X/0.65
  • HI PLAN 63X/0.75

Applications:

  • Hands-on instruction and training for new users
  • Consultation and to obtain a second opinion from other experts during tissue sample imaging

PC workstation for offline image processing and analysis

One PC workstation for offline image analysis

One PC workstation for offline image analysis

 

o   Intel Core i7 5820K 3.3GHz 6-core processor

o   128GB SSD (Boot Drive) & 1TB HDD (Storage Drive)

o   32GB Memory

o   AMD R9 290X Graphics Card for 3D visualisation

o   ImageJ/Fiji

o   Metamorph 7.7.7

o   Nikon NIS Elements AR offline

o   Zen Blue 2012 Lite

o   Cell Profiler