The Advanced Optical Microscopy Facility

Accelerate your research by tapping into a world-class imaging facility

Get Started

The Advanced Optical Microscopy Facility

Accelerate your research by tapping into a world-class imaging facility

Get Started

Welcome to the AOMF


The Advanced Optical Microscopy Facility in Toronto, Canada, serves University Health Network researchers as well as external academic and industrial users. With over 40 instruments at 4 sites, the AOMF is equipped for nearly any optical microscopy experiment including: confocal, multiphoton, super-resolution, FRAP, FRET, live-cell timelapse, whole-slide scanning, image analysis and more.

Founded in 2002

18

years of experience

Trusted by over

600

users a year

With over

40

instruments

Locations
Go to PMCT map
Go to TGH map
Go to WCIF map
Go to PM map

Services

Get started by booking your free consultationIcon image of rocket

Free Consultations

+

Free Consultations

  • Book a free consultation with our experienced staff to tour the AOMF and discuss your project.
  • This ensures that we set you up on the most appropriate instrument.

Training and Support

+

Training and Support

  • Our individual hands-on training sessions are 1 to 4 hours in length, and cost $65 to $100/hr (see fee schedule).
  • Maximum 2 trainees per session (the 2nd receives a 50% discount).

Whole-slide Scanning

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Whole-slide Scanning

  • Our staff use industry-leading Aperio and Zeiss scanners to digitize your entire brightfield and fluorescence tissue sections at 0.5um resolution (high-resolution 20x objective) or better.
  • Typical turnaround time is 2 days (brightfield) to 1 week (fluorescence).
  • Prices start at $8/slide.

Full-service Image Capture

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Full-service Image Capture

  • Want to capture a few quick images without taking the time to get trained?
  • Book a full service session and one of our experienced staff will operate the instrument while you help choose the appropriate fields of view.

Courses and Workshops

+

Courses and Workshops

  • From our 2-hr Fundamentals of Microscopy course to our week-long Comprehensive Course on Fluorescence Microscopy, develop your optical microscopy expertise with our hands-on courses and workshop.

Image Analysis and Quantification

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Image Analysis and Quantification

Let us help you produce meaningful data from your images!

  • FIJI ImageJ: 2D analysis on your own computer
  • Imaris (by Bitplane): 3D rendering and analysis including co-localization, tracking, and filament tracing
  • Halo (by Indica Labs): whole-slide analysis for both brightfield and fluorescence tissues, including AI Classifier, TMA analysis, CytoNuclear quantification and more.

Services

Get started by booking your free consultationIcon image of

Free Consultations

+

Free Consultations

  • Book a free consultation with our experienced staff to tour the AOMF and discuss your project.
  • This ensures that we set you up on the most appropriate instrument.

Training and Support

+

Training and Support

  • Our individual hands-on training sessions are 1 to 4 hours in length, and cost $65 to $100/hr (see fee schedule).
  • Maximum 2 trainees per session (the 2nd receives a 50% discount).

Whole-slide Scanning

+

Whole-slide Scanning

  • Our staff use industry-leading Aperio and Zeiss scanners to digitize your entire brightfield and fluorescence tissue sections at 0.5um resolution (high-resolution 20x objective) or better.
  • Typical turnaround time is 2 days (brightfield) to 1 week (fluorescence).
  • Prices start at $8/slide.

Full-service Image Capture

+

Full-service Image Capture

  • Want to capture a few quick images without taking the time to get trained?
  • Book a full service session and one of our experienced staff will operate the instrument while you help choose the appropriate fields of view.

Courses and Workshops

+

Courses and Workshops

  • From our 2-hr Fundamentals of Microscopy course to our week-long Comprehensive Course on Fluorescence Microscopy, develop your optical microscopy expertise with our hands-on courses and workshop.

Image Analysis and Quantification

+

Image Analysis and Quantification

Let us help you produce meaningful data from your images!

  • FIJI ImageJ: 2D analysis on your own computer
  • Imaris (by Bitplane): 3D rendering and analysis including co-localization, tracking, and filament tracing
  • Halo (by Indica Labs): whole-slide analysis for both brightfield and fluorescence tissues, including AI Classifier, TMA analysis, CytoNuclear quantification and more.

Instruments

Icon image of confocal

Confocal / Multiphoton

Confocal and multiphoton (two-photon) microscopes use lasers to excite fluorescence, and exclude out-of-focus light to image slices or “optical sections” of the specimen that can be thinner than 1um. Confocals are the AOMF’s most popular instruments. Most are equipped for live cells, and some have special capabilities such as super-resolution, fast resonant scanning, or extra-sensitive GaAsP/HyD detectors.

confocal image
▸ Zeiss LSM700 Confocal (PMCRT)
Model Zeiss LSM700 Confocal microscope
Zeiss AxioObserver 200M inverted stand
Lasers, fluorophores 405nm (DAPI, Hoechst, Alexa405)
488nm (Alexa488, Cy2, FITC, GFP)
555nm (Alexa555, Alexa568, Alexa594, Cy3, DsRed, TxRed, RFP, mCherry)
639nm (Alexa 647, Cy5)
Objective lenses FLUAR 5x/0.25 NA
FLUAR 10x/0.50 NA
Plan-Apochromat 20x/0.8 NA
Plan-Apochromat 40x/1.4 NA oil immersion
Plan-Apochromat 63x/1.4 NA oil immersion
C-APO 63x/1.2 NA water immersion
Detectors 2 standard sensitivity PMT detectors (multiplexing for up to 4 channels sequentially)
Transmitted-light PMT
Filters Fully spectral, 400 to 700nm
Incubation None
Advantages and techniques High-resolution confocal
Spectral unmixing
Software Zeiss Zen software (free download)
FIJI ImageJ (free download – 2D analysis)
Imaris by Bitplane (offline, licensed)
Huygens deconvolution (offline, licensed)
▸ Zeiss LSM710 Confocal and Multiphoton (PMCRT)
Model Zeiss LSM710 Confocal and multiphoton (two-photon) microscope
Zeiss AxioExaminer upright stand
Lasers, fluorophores 405nm (DAPI, Hoechst, Alexa405)
488nm (Alexa488, Cy2, FITC, GFP)
555nm (Alexa555, Alexa568, Alexa594, Cy3, DsRed, TxRed, RFP, mCherry)
639nm (Alexa 647, Cy5)
Objective lenses FLUAR 5x/0.25 NA
FLUAR 10x/0.50 NA
Plan-Apochromat 20x/0.8 NA
Plan-Apochromat 40x/1.4 NA oil immersion
Plan-Apochromat 63x/1.4 NA oil immersion
C-APO 63x/1.2 NA water immersion
Detectors 2 standard sensitivity PMT detectors (multiplexing for up to 4 channels sequentially)
Transmitted-light PMT
Filters Fully spectral, 400 to 700nm
Incubation None
Advantages and techniques High-resolution confocal
Spectral unmixing
Software Zeiss Zen software (free download)
FIJI ImageJ (free download – 2D analysis)
Imaris by Bitplane (offline, licensed)
Huygens deconvolution (offline, licensed)
▸ Leica SP8 Confocal (PMCRT)
Model Leica TCS SP8 Confocal microscope
Leica DMi8 CS inverted stand
Lasers, fluorophores 405nm (DAPI, Hoechst, Alexa405)
488nm (Alexa488, Cy2, FITC, GFP)
552nm (Alexa555, Alexa568, Alexa594, Cy3, DsRed, TxRed, RFP, mCherry)
638nm (Alexa 647, Cy5)
Objective lenses HC PL FLUOTAR 5x/0.15 NA
HC PL APO 10x/0.40 NA CS2
HC PL APO 20x/0.75 NA CS2
HCX PL APO 40x/0.85 NA CS, Corr 0.11 – 0.23mm
HC PL APO 63x/1.40 NA Oil immersion CS2
Detectors 3 standard sensitivity PMT detectors + 2 HyD high-sensitivity detectors
Transmitted-light PMT
Filters Fully spectral, 400 to 700nm
Incubation None
Advantages and techniques High-resolution confocal
Spectral unmixing
Tiling / Stage Overview
AFC hardware autofocus
Software Leica LAS-X software (free download)
FIJI ImageJ (free download – 2D analysis)
Imaris by Bitplane (offline, licensed)
Huygens deconvolution (offline, licensed)
▸ Leica STED Confocal and Super-resolution (PMCRT)
Model Leica TCS SP8 STED3X Confocal and Super-resolution microscope
Leica DMi8 CS inverted stand
Picoquant FLIM / FCS
Lasers, fluorophores 405nm (DAPI, Hoechst, Alexa405)
440nm (CFP)
White Light Laser (WLL), 475-675nm in 1nm steps (Alexa 488 to Cy5 and everything in between)
Objective lenses HC PL APO 10x/0.40 NA CS2
HC PL APO 20x/0.75 NA CS2
HC PL APO 63x/1.40 NA Oil immersion CS2
HC PL APO 63x/1.20 NA Water immersion CS2 motCorr (by request)
HC PL APO 93x/1.30 NA Glycerol immersion CS2 motCorr
HC PL APO 100x/1.40 NA Oil immersion CS2
Detectors 3 standard sensitivity PMT detectors + 2 HyD high-sensitivity detectors
Transmitted-light PMT
Filters Fully spectral, 400 to 700nm
Incubation Tokai Hit stage-top incubator
Advantages and techniques High-resolution confocal of fixed and live cells
STED super-resolution with 592nm, 660nm, and 775nm depletion lasers
Fluorescence Lifetime Imaging Microscopy (FLIM)
Fluorescence Correlation Spectroscopy (FCS)
Hyvolution 2 deconvolution
Spectral unmixing
Tiling / Stage Overview
AFC hardware autofocus
Software Leica LAS-X software (free download)
FIJI ImageJ (free download – 2D analysis)
Imaris by Bitplane (offline, licensed)
Huygens deconvolution (offline, licensed)
▸ Nikon A1R Confocal (TGH)
Model Nikon A1R Confocal microscope with resonant scanner
Nikon Eclipse Ti inverted stand
Lasers, fluorophores 405nm (DAPI, Hoechst, Alexa405)
445nm (CFP)
488nm (Alexa488, Cy2, FITC, GFP)
514 nm (YFP)
561nm (Alexa555, Alexa568, Alexa594, Cy3, DsRed, TxRed, RFP, mCherry)
640nm (Alexa 647, Cy5)
Objective lenses Plan Apo 10x/0.45 NA
Plan Apo 20x/0.75 NA
Plan FL 40x/1.3 NA oil
Plan Apo, nano-crystal, 60x/1.4 NA, oil immersion
Plan Apo, IR, 60x/1.7 NA, water immersion
NIR Apo 40x/0.8 NA, water immersion
Detectors 2 standard PMT detectors + 2 GaAsP high-sensitivity detectors
Transmitted-light PMT
Filters Fully spectral, 400 to 750nm
Incubation OKO Lab stage-top incubator
Advantages and techniques High-Speed resonant scanning confocal for imaging dynamics; and standard galvanometer scanning mirrors for high-quality imaging of fixed samples
MCL nano-drive allows fast Z-stack imaging
Live cell imaging
Perfect focus hardware autofocus system
Software Nikon Element software (free download)
FIJI ImageJ (free download – 2D analysis)
Imaris by Bitplane (offline, licensed)
Huygens deconvolution (offline, licensed)
▸ Olympus FV1000_A Confocal (TGH)
Model Olympus Fluoview 1000 Confocal microscope
Olympus IX81 inverted stand
Lasers, fluorophores 405nm (DAPI, Hoechst, Alexa405)
458nm (CFP)
488nm (Alexa488, Cy2, FITC, GFP)
515 nm (YFP)
543nm (Alexa555, Alexa568, Alexa594, Cy3, DsRed, TxRed, RFP, mCherry)
633nm (Alexa 647, Cy5)
Objective lenses UPlan Apo 10x/0.40 NA
UPlan SApo 20x/0.75NA
UPlan SApo 40x/0.95 NA
LUM Plan FL 40x/0.8 NA water immersion
Plan Apo 63x/1.42 NA oil immersion
Detectors 3 standard sensitivity PMT detectors
Transmitted-light PMT
Filters Fully spectral, 400 to 750nm
Incubation Solent Scientific incubation Chamber
Advantages and techniques SIM scanner allows fast photobleaching and simultaneous imaging
Spectral unmixing
Live cell imaging
Software Olympus software
FIJI ImageJ (free download – 2D analysis)
▸ Olympus FV1000_B Confocal (TGH)
Model Olympus Fluoview 1000 Confocal microscope
Olympus IX81 inverted stand
Lasers, fluorophores 405nm (DAPI, Hoechst, Alexa405)
473nm (Alexa488, Cy2, FITC, GFP)
559nm (Alexa555, Alexa568, Alexa594, Cy3, DsRed, TxRed, RFP, mCherry)
635nm (Alexa 647, Cy5)
Objective lenses UPlan SApo 4x/0.16 NA
UPlan Apo 10x/0.40 NA
UPlan SApo 20x/0.75NA
UPlan FL 20x/0.5 NA
UPlan SApo 40x/0.95 NA
Plan Apo 40x/1.35 NA oil immersion
Plan Apo 63x/1.42 NA oil immersion
Detectors 4 standard sensitivity PMT detectors
Transmitted-light PMT
Filters Fully spectral, 400 to 750nm
Incubation LCI Stage incubator
Advantages and techniques SIM scanner allows fast photobleaching and simultaneous imaging
Spectral unmixing
Live cell imaging
Software Olympus software
FIJI ImageJ (free download – 2D analysis)
▸ WaveFX Spinning-disk Confocal (TGH)
Model Yokogawa CSU-10 Spinning-disk confocal
Olympus IX81 inverted stand
Lasers, fluorophores 405nm (DAPI, Hoechst, Alexa405)
491nm (Alexa488, Cy2, FITC, GFP)
561nm (Alexa555, Alexa568, Alexa594, Cy3, DsRed, TxRed, RFP, mCherry)
640nm (Alexa 647, Cy5)
730 nm (Alexa 700, Alexa 750, Cy7)
Objective lenses UPlan FL 10x/0.30 NA
UPlan SApo 20x/0.75NA
UPlan FL 40x/0.75 NA
UPlan Apo 60x/1.2 NA water immersion
Plan Apo 63x/1.4 NA oil immersion
Camera Hamamatsu EM-CCD C9100-13
Incubation LCI Stage incubator
Advantages and techniques Piezo Z-axis stage allows fast z-stack imaging
Live cell imaging
Software Volocity software
FIJI ImageJ (free download – 2D analysis)
▸ Olympus FV1000_C Confocal (PM)
Model Olympus Fluoview 1000 Confocal microscope
Olympus IX81 inverted stand
Lasers, fluorophores 405nm (DAPI, Hoechst, Alexa405)
458nm (CFP)
488nm (Alexa488, Cy2, FITC, GFP)
543nm (Alexa555, Alexa568, Alexa594, Cy3, DsRed, TxRed, RFP, mCherry)
633nm (Alexa 647, Cy5)
Objective lenses UPlan Apo 10x/0.40 NA
UPlan SApo 20x/0.75NA
UPlan SApo 40x/0.95 NA
Plan Apo 40x/1.30 NA Oil immersion
Plan Apo 60x/1.42 NA Oil immersion
Plan Apo 60x/1.20 Water immersion
Detectors 4 standard sensitivity PMT detectors
Transmitted-light PMT
Filters Fully spectral, 400 to 700nm
Incubation None
Advantages and techniques High-resolution imaging of fixed cells and tissues
Software Olympus software
FIJI ImageJ (free download – 2D analysis)
▸ WaveFX Spinning-disk Confocal (PM)
Model Yokogawa CSU-10 Spinning-disk confocal
Olympus IX81 inverted stand
Lasers, fluorophores 405nm (DAPI, Hoechst, Alexa405)
491nm (Alexa488, Cy2, FITC, GFP)
561nm (Alexa555, Alexa568, Alexa594, Cy3, DsRed, TxRed, RFP, mCherry)
640nm (Alexa 647, Cy5)
Objective lenses UPlan FL 10x/0.30 NA
UPlan SApo 20x/0.75NA
UPlan FL 40x/0.75 NA
UPlan Apo 60x/1.2 NA water immersion
Plan Apo 63x/1.4 NA oil immersion
Camera Hamamatsu EM-CCD C9100-13
Incubation LCI Stage incubator
Advantages and techniques Piezo Z-axis stage allows fast z-stack imaging
Live cell imaging
Software Volocity software
FIJI ImageJ (free download – 2D analysis)
▸ Zeiss LSM880 Confocal with Airyscan (Krembil)
Model Zeiss LSM880 Confocal microscope with AiryScan
Zeiss AxioObserver Stand
Lasers, fluorophores 405nm (DAPI, Hoechst, Alexa405)
488nm (Alexa488, Cy2, FITC, GFP)
555nm (Alexa555, Alexa568, Alexa594, Cy3, DsRed, TxRed, RFP, mCherry)
639nm (Alexa 647, Cy5)
Objective lenses Plan-Apochromat 10x/0.45 NA
Plan-Apochromat 20x/0.80 NA
Plan-Apochromat 40x/0.95 NA
Plan-Apochromat 63x/1.4 NA oil immersion
Detectors 2 standard sensitivity PMT detectors
1 high-sensitivity GaAsP detector
Filters Fully spectral, 400 to 700nm
Incubation Cell culture and 24-well plate format
Advantages and techniques High-resolution and extended resolution (AiryScan) confocal
Spectral unmixing
Live cell confocal imaging – FRET, FRAP
Software Zeiss Zen software (free download)
FIJI ImageJ (free download – 2D analysis)
Imaris by Bitplane (offline, licensed)
Huygens deconvolution (offline, licensed)
▸ Leica SP8 Confocal and Multiphoton (Krembil)
Model Leica TCS SP8 MP Confocal and multiphoton microscope
Leica DM8 physiological upright stand
Lasers, fluorophores Coherent Chameleon Discovery Laser
  • 2P/3P SHG/THG Imaging
  • Tunable beam 680-1300
  • Fixed beam output 1040 nm
488nm (Alexa488, Cy2, FITC, GFP)
555nm (Alexa555, Alexa568, Alexa594, Cy3, DsRed, TxRed, RFP, mCherry)
Objective lenses HC-IRAPO 25X / 1.0 NA water dipping lens
Detectors 2 Internal detectors
  • 1 PMT
  • 1 HyD High efficiency detector
4 Nondescanned detectors
  • 2 PMT
  • 2 HyD High efficiency detectors
Filters Fully spectral, 400 to 700nm
Incubation Thermal plate
Advantages and techniques In vivo imaging
High-resolution confocal
High-speed resonant confocal
Multiphoton imaging for deep tissue penetration
Spectral unmixing
Second- and Third-harmonic generation imaging
Software Leica LAS-X (Free download)
FIJI ImageJ (free download – 2D analysis)
Imaris by Bitplane (offline, licensed)
Huygens deconvolution (offline, licensed)
Icon image of scanning

Whole-slide scanners

For tissue sections from 4um to 12um thick, AOMF staff will digitize your entire slide at high resolution starting at just $8/slide for brightfield and $12/slide for fluorescence (see Fees). The resulting images range from 100MB to 10GB per slide, and therefore special (free) software is required for viewing them. Applications include virtual microscopy (pan, zoom, and “snap” a picture of any field of view) and whole-slide analysis (proprietary HALO software required).

whole-slide scanning images
▸ Aperio AT2 brightfield scanner (PMCRT, drop-box at Krembil)
Model Aperio AT2 brightfield scanner (Leica Biosystems
400 slide capacity
Objective lens UPlanS Apo 20x / 0.75 NA (high-resolution 20x objective)
2x doubler for 40x
Pixel Size / Resolution 20x: 0.5µm/pixel
40x: 0.25µm/pixel
Input slide sizes Standard slide: 1” x 3”
Whole-mount slide: 2” x 3”
Turn-around time Typically 2 to 5 business days
Software Aperio Imagescope software (free download)
Halo by IndicaLabs (offline, licensed)
▸ Zeiss AxioScan fluorescence scanner (PMCRT, drop-box at Krembil)
Model Zeiss AxioScan
100 slide capacity
Filters / fluorophores Chroma ET DAPI 49000 (DAPI)
Chroma ET EGFP 49002 (Alexa488, Cy2, FITC, GFP)
Chroma ET CY3/TRITC 49004 (Alexa555, Alexa568, Cy3, DsRed, RFP)
Chroma ET mCherry TexasRed 49008 (Alexa594, TexasRed, mCherry)
Chroma ET Cy5 49006 (Alexa 647, Cy5)
* Note users must choose either Cy3 or TxRed probe, not both
Objective lens Fluar 2.5x / 0.12 NA
Plan Apochromat 5x / 0.16 NA
Plan Apochromat 10x / 0.45 NA
Plan Apochromat 20x / 0.80 NA
Plan Apochromat 40x / 0.95 NA
Pixel Size / Resolution Standard resolution: 20x (0.25µm/pixel)
High resolution: 40x: (0.12µm/pixel)
Input slide sizes Standard slide: 11” x 31”
Whole-mount slide: 21” x 31”
Turn-around time Typically 5 to 10 business days
Software Zeiss Zen software (free download)
Halo by Indica Labs (offline, licensed)
▸ HALO whole-slide analysis software (PMCRT, PM, and Krembil)
Licenses 5-seat license for HALO
1 demo license for HALO-AI Deep Learning (expires Jan 2021)
Locations 5 local licenses are installed on high-end desktop computers
  • PMCRT Room 15-301 (IQ4 and IQ5 analysis stations)
  • PMCRT 7th floor (STTARR)
  • WCIF (Krembil, 7th floor)
  • PM (610 University, 7th floor)
Modules / Add-ons Tissue Classifier
Tissue Microarray (TMA)
Serial Section Analysis
Batch analysis (typically 50 slides can be analyzed overnight)
Cytonuclear IHC / Cytonuclear FL
Area Quantification / Area Quantification FL
Object Colocalization / Object Colocalization FL
Vacuole
Islet IHC / Islet FL
Highplex FL / Multiplex IHC
ISH (RNAScope) / FISH (RNAScope)
File Formats Aperio (SVS, AFI)
Zeiss (CZI)
3D Histech (MRXS)
Hamamatsu (NDPI, NDPIS)
Nikon (ND2)
Olympus (VSI)
Leica (SCN, LIF)
Ventana (BIF)
Perkin Elmer (QPTIFF, component TIFF)
Non-proprietary (JPG, TIF)
Typical workflow
  1. Copy the images you want to analyze to the local data drive, and add them to a Study (database) in HALO.
  2. Use Tissue Classifier to identify the areas/patterns you want to analyze. For example, with a few strokes of the pen tool you define tumour, stroma, and background regions and the classifier separates them.
  3. Regions of interest can also be defined with pen, negative pen (exclusion), or magnet tools.
  4. Choose an analysis module and fine-tune the settings. For example, Cytonuclear specifically finds cells (using nuclear stain), and measures nuclear or membrane labeling for each cell.
Icon image of microscope

Widefield

For applications that don’t demand confocal microscopy, our widefield fluorescence microscopes incorporate motorization and high-end components beyond what you would find in a typical lab. Most are equipped with fast, high-resolution cameras, and some have full incubator boxes for long-term timelapse imaging, or macroscope lenses for large fields of view. Available contrasts include fluorescence, brightfield, phase contrast, Differential Interference Contrast (DIC), polarized light, and darkfield.

widefield images
▸ Zeiss AxioObserver Widefield (PMCRT)
Model Zeiss AxioObserver.Z1 inverted stand
Light source X-Cite 120Q metal halide fluorescence lamp
Filter sets
  1. DAPI, Hoechst, Alexa405 (Chroma 39000 AT)
  2. Alexa488, Cy2, FITC, GFP (Chroma 49002 ET)
  3. Alexa555, Alexa568, Alexa594, Cy3, DsRed (Chroma 49004 ET)
  4. TexasRed, mCherry (Chroma 49008 ET)
  5. Alexa 647, Cy5 (Chroma 49019 ET longpass)
  6. CFP (Ex 436/10, Em 470LP) – available upon request
  7. YFP (Ex 500/20, Em 535/30) – available upon request
  8. Reflected light – available upon request
Objective lenses Fluar 5x/0.25 NA
Plan-Apochromat 10x/0.45 NA Phase Contrast
Plan-Apochromat 20x/0.80 NA
Plan-Apochromat 40x/0.95 NA
LD A-Plan 32X/0.40 NA Long working distance (plastic) phase contrast
Plan-Apochromat 63x/1.4 NA oil immersion – available upon request
Camera Hamamatsu ORCA-Flash 4.0 (4 MP sCMOS camera)
Incubation LCI Chamlide stage-top incubator with inserts for LabTek, Ibidi, Eppendorf, MatTek, and 24-well plates
Advantages and techniques Fixed slides (widefield immunofluorescence)
Live cell imaging, both fluorescence and phase contrast/DIC
High-speed widefield imaging
Tiling/stitching
Fluorescence, phase contrast, DIC
Software Zeiss Zen software (free download)
FIJI ImageJ (free download – 2D analysis)
▸ Zeiss AxioImager Widefield (PMCRT)
Model Zeiss AxioImager.Z1 upright stand
Light source X-Cite eXacte metal halide fluorescence lamp
Filter sets Narrow cubes optimized for FISH
  1. DAPI, Hoechst, Alexa405 (Chroma 49000 ET)
  2. Aqua, CFP (Chroma 49302)
  3. Alexa488, Cy2, FITC, GFP (Chroma 49303 ET)
  4. Gold, YFP (Chroma 49304 ET)
  5. Alexa555, Alexa568, Alexa594, Cy3, DsRed (Chroma 49305 ET)
  6. TexasRed, mCherry (Chroma 49306 ET)
  7. Alexa 647, Cy5 (Chroma 49009 ET narrow)
  8. FITC Longpass (Chroma 49012: Ex 480/40, Em 500LP)
  9. Cy3 Longpass (Chroma 49016: Ex 545/25, Em 570LP)
  10. Qdot Longpass (Ex 460SP, Em 500LP) – available upon request
  11. DAPI/FITC/TRITC triple filter – available upon request
Objective lenses EC Plan-Neofluar 10x/0.3
Plan Neofluar 16x/0.5 NA multi-immersion
Plan-Neofluar 20x/0.5 NA
Plan-Neofluar 40x/0.75 NA
Plan-Apochromat 63x/1.4 NA oil immersion
Plan-Neofluar 100x/1.3 NA oil immersion
Cameras Hamamatsu ORCA-Flash 4.0 (4 MP sCMOS camera)
CRI Nuance spectral camera (available upon request)
Advantages and techniques Fixed slides (widefield immunofluorescence)
Fluorescence In Situ Hybridization (FISH)
Software Zeiss Zen software (free download)
FIJI ImageJ (free download – 2D analysis)
▸ Zeiss AxioZoom Macroscope (PMCRT)
Model Zeiss AxioZoom.V16 upright macroscope
Light source X-Cite eXacte metal halide lamp
Filter sets
  1. DAPI, Hoechst, Alexa405 (Zeiss #49, Ex 365, Em 445/50)
  2. Alexa488, Cy2, FITC, GFP (Zeiss #38HE, Ex 470/40, Em 525/50)
  3. Alexa568, Alexa594, Cy3, DsRed, TxRed, mCherry (Chroma 49008)
  4. Cy5, Alexa 647 (Chroma 49006, Ex 620/60, Em 700/75)
Objective lenses Plan Neofluar Z 1X/0.25 NA
Camera Hamamatsu ORCA-Flash 4.0 (4 MP sCMOS camera)
Incubation None
Advantages and techniques Large FOV imaging
Widefield fluorescence stitching and tiling
Gross specimen imaging
Software Zeiss Zen software (free download)
FIJI ImageJ (free download – 2D analysis)
▸ Olympus BX51 Widefield (PMCRT)
Model Olympus BX51 upright stand
Light source Halogen transmitted-light lamp
Objective lenses UPlanSApo 4x / 0.16 NA
UPlanFl 10x/0.3 NA
UPlanApo 20x/0.7 NA
UPlanFl 40x/0.75 NA
PlanApo 60x/1.4 NA oil immersion
Camera Lumenera Infinity 3-6URC colour camera (6MP)
Advantages and techniques Fixed slides, transmitted light
Brightfield (consider slide scanning instead)
Polarized light
Darkfield
Software Micromanager
FIJI ImageJ (free download – 2D analysis)
▸ Leica Stereomicroscope (PMCRT)
Model Leica MZFLIII upright stereomicroscope
Light sources X-Cite 120 metal halide lamp (fluorescence)
Intralux 5000 halogen (transmitted / reflected light)
Filter sets
  1. Alexa488, Cy2, FITC, GFP (Ex 470/40, Em 500LP)
  2. Alexa568, Alexa594, Cy3, DsRed, TxRed, mCherry (Ex 560/55, Em 645/75)
Objective lenses PlanApo 0.8 to 10x / 0.12 NA
Macro lens
Camera Lumenera Infinity 3-6URFC colour camera (6MP)
Advantages and techniques Dissecting
Large FOV imaging
Gross specimen imaging
Software Micromanager software
FIJI ImageJ (free download – 2D analysis)
▸ Zeiss AxioObserver_TGH Widefield (TGH)
Model Zeiss AxioObserver.Z1 inverted stand
Light source X-Cite 120 metal halide lamp
Filter sets
  1. DAPI, Hoechst, Alexa405
  2. Alexa488, Cy2, FITC, GFP
  3. Alexa555, Alexa568, Alexa594, Cy3, DsRed, TxRed, RFP, mCherry
  4. Alexa 647, Cy5
Objective lenses Plan-Apochromat 5x/0.15 NA PH1
Fluar 10x/0.5 NA
Plan-Apochromat 10x/0.25 NA PH1
Plan-Apochromat 20x/0.80 NA
Plan-Apochromat 63x/1.4 NA oil immersion
Camera Hamamatsu ORCA-Flash 4.0 (4 MP sCMOS camera)
Incubation Full PECON incubation chamber with O2 module
Advantages and techniques Live cell imaging
Multi-location timelapse imaging (up to 48 hours)
Definite focus hardware autofocus system
Widefield immunofluorescence
Software Zeiss Zen software (free download)
FIJI ImageJ (free download – 2D analysis)
▸ Zeiss AxioImager_PM Widefield (PM)
Model Zeiss AxioImager.Z1 upright stand
Light source X-Cite 120 LED fluorescence lamp
Filter sets
  1. DAPI, Hoechst, Alexa405 (Zeiss #49)
  2. CFP (Zeiss #47)
  3. Alexa488, Cy2, FITC, GFP (Zeiss #38 HE)
  4. Alexa555, Alexa568, Alexa594, Cy3, DsRed (Zeiss #20 HE)
  5. TexasRed, mCherry (Zeiss #45)
  6. Alexa 647, Cy5 (Zeiss #50)
Objective lenses Plan-Apochromat 10x/0.45 NA
Plan-Apochromat 20x/0.8 NA
EC Plan-Neofluar 40x/0.75 NA
Plan-Apochromat 40x/1.3 NA oil immersion
Plan-Apochromat 63x/1.4 NA oil immersion
Plan-Neofluar 100x/1.4 NA oil immersion
Camera Hamamatsu ORCA-Flash 4.0 (4 MP sCMOS camera)
Advantages and techniques Fixed slides (widefield immunofluorescence)
Tiling and stitching
Software Zeiss Zen software (free download)
FIJI ImageJ (free download – 2D analysis)
▸ Leica Stereomicroscope_PM (PM)
Model Leica MZ16F upright stereomicroscope
Light source X-Cite 120 metal halide lamp (fluorescence)
Intralux 5000 halogen (transmitted / reflected light)
Filter sets
  1. CFP
  2. Alexa488, Cy2, FITC, GFP
  3. Alexa568, Alexa594, Cy3, DsRed, TxRed, mCherry
  4. YFP
Objective lenses PlanApo 0.7 to 11x / 0.12 NA
Camera Leica DCF500
Advantages and techniques Dissecting
Large FOV imaging
Gross specimen imaging
Software Leica software
FIJI ImageJ (free download – 2D analysis)
▸ Leica DMI Widefield (PM)
Model Leica DMIRB inverted stand
Light source X-Cite 120 LED
Filter sets
  1. DAPI, Hoechst, Alexa405
  2. Alexa488, Cy2, FITC, GFP
  3. Alexa555, Alexa568, Alexa594, Cy3, DsRed, TxRed, RFP, mCherry
Objective lenses Fluotar 2.5x / 0.07 NA
NPlan 10x/0.22 NA PH1
NPlan LWD 20x/0.40 NA PH1
NPlan LWD 40x/0.55 NA PH2
Camera Hamamatsu ORCA-Flash 4.0 LT (4 MP sCMOS camera)
Incubation None
Advantages and techniques Low-resolution live cell imaging
Fluorescence, phase contrast
Software Zeiss Zen software (free download)
FIJI ImageJ (free download – 2D analysis)
▸ Zeiss AxioObserver_WCIF Widefield (Krembil)
Model Zeiss AxioObserver 7 inverted stand
Light source X-Cite 120 LED Mini
Filter sets
  1. DAPI, Hoechst, Alexa405 (Ex 340, Em 460/50)
  2. CFP, Cerulean (Ex 436/20, Em 470/24)
  3. Alexa488, Cy2, FITC, GFP (Ex 470/40, Em 525/50)
  4. YFP, Venus (Ex 500/20, Em 525/30)
  5. Alexa555, Alexa568, Alexa594, Cy3, DsRed (Ex 545/25, Em 605/70)
  6. TxRed, RFP, mCherry (Ex 560/40, Em 625/30)
  7. Alexa 647, Cy5 (Ex 640/30, Em 690/50)
  8. Fura 2 (Ex 340, Ex 380, Em 425 LP)
Objective lenses Fluar 5x/0.25 NA
Plan-Apochromat 10x/0.45 NA
Plan-Apochromat 20x/0.80 NA
Plan-Apochromat 40x/0.95 NA
LD Achroplan 40X/0.60 NA Long working distance (plastic) phase contrast
Plan-Apochromat 63x/1.4 NA oil immersion
Camera Hamamatsu ORCA-Flash 4.0 (4 MP sCMOS camera)
Incubation Cell culture and 24-well plate format
Advantages and techniques Fixed cells (widefield immunofluorescence)
Live cell imaging
High-speed widefield imaging
Multi-location timelapse imaging
Calcium imaging
Tiling/stitching
Fluorescence, phase contrast, DIC
Software Zeiss Zen software (free download)
FIJI ImageJ (free download – 2D analysis)
Imaris by Bitplane (licensed)
Huygens deconvolution (licensed)
▸ Zeiss AxioZoom_WCIF Macroscope (Krembil)
Model Zeiss AxioZoom.V16 upright macroscope
Light source X-Cite 120 metal halide lamp
Filter sets
  1. DAPI, Hoechst, Alexa405 (Zeiss #49, Ex 365, Em 445/50)
  2. Alexa488, Cy2, FITC, GFP (Zeiss #38HE, Ex 470/40, Em 525/50)
  3. Alexa568, Alexa594, Cy3, DsRed, TxRed, mCherry (Zeiss #63HE, Ex 572/25, Em 629/62)
Objective lenses Plan Neofluar Z 1X/0.25 NA
Camera Hamamatsu ORCA-Flash 4.0 (4 MP sCMOS camera)
Incubation None
Advantages and techniques Large FOV imaging
Widefield fluorescence stitching and tiling
Gross specimen imaging
Software Zeiss Zen software (free download)
FIJI ImageJ (free download – 2D analysis)
Icon image of mouse

In vivo / intravital

A comprehensive investigation of cancer genes and selected non-cancer genes within patient blood and tumour samples can provide information about diagnosis, patient risk stratification and response to therapy, as well as help determine potential application of targeted therapies for different malignancies.

in vivo image
▸ Zeiss LSM710 Confocal and Multiphoton (PMCRT)
Model Zeiss LSM710 Confocal and multiphoton (two-photon) microscope
Zeiss AxioExaminer upright stand
Coherent Chameleon Discovery femtosecond laser
Lasers, fluorophores Single-photon excitation:
  • 405nm (DAPI, Hoechst, Alexa405)
  • 488nm (Alexa488, Cy2, FITC, GFP)
  • 555nm (Alexa555, Alexa568, Alexa594, Cy3, DsRed, TxRed, RFP, mCherry)
  • 639nm (Alexa 647, Cy5)
Two-Photon excitation:
  • Fixed beam 1040nm
  • Tunable beam 680 to 1300nm
  • GDD dispersion compensation
Objective lenses FLUAR 5x/0.25 NA
FLUAR 10x/0.50 NA
Plan-Apochromat 20x/0.8 NA
Plan-Apochromat 40x/1.4 NA oil immersion
Plan-Apochromat 63x/1.4 NA oil immersion
C-APO 63x/1.2 NA water immersion
Detectors 2 standard sensitivity PMT detectors (multiplexing for up to 4 channels sequentially)
Transmitted-light PMT
Filters Fully spectral, 400 to 700nm
Incubation None
Advantages and techniques High-resolution confocal
4-channel multiphoton for deeper penetration into thick specimens
Spectral unmixing
Second Harmonic Generation (SHG) for imaging collagen
Third Harmonic Generation (THG) for imaging lipids
Software Zeiss Zen software (free download)
FIJI ImageJ (free download – 2D analysis)
Imaris by Bitplane (offline, licensed)
Huygens deconvolution (offline, licensed)
▸ Leica Stereomicroscope (PMCRT)
Model Leica MZFLIII upright stereomicroscope
Light Sources X-Cite 120 metal halide lamp (fluorescence)
Intralux 5000 halogen (transmitted / reflected light)
Filter sets
  1. Alexa488, Cy2, FITC, GFP (Ex 470/40, Em 500LP)
  2. Alexa568, Alexa594, Cy3, DsRed, TxRed, mCherry (Ex 560/55, Em 645/75)
Objective lenses PlanApo 0.8 to 10x / 0.12 NA
Macro lens
Camera Lumenera Infinity 3-6URFC colour camera (6MP)
Advantages and techniques Dissecting
Large FOV imaging
Gross specimen imaging
Software Micromanager software
FIJI ImageJ (free download – 2D analysis)
▸ Zeiss AxioZoom Macroscope (PMCRT)
Model Zeiss AxioZoom.V16 upright macroscope
Light Source X-Cite eXacte metal halide lamp
Filter sets
  1. DAPI, Hoechst, Alexa405 (Zeiss #49, Ex 365, Em 445/50)
  2. Alexa488, Cy2, FITC, GFP (Zeiss #38HE, Ex 470/40, Em 525/50)
  3. Alexa568, Alexa594, Cy3, DsRed, TxRed, mCherry (Chroma 49008)
  4. Cy5, Alexa 647 (Chroma 49006, Ex 620/60, Em 700/75)
Objective lenses Plan Neofluar Z 1X/0.25 NA
Camera Hamamatsu ORCA-Flash 4.0 (4 MP sCMOS camera)
Incubation None
Advantages and techniques Large FOV imaging
Widefield fluorescence stitching and tiling
Gross specimen imaging
Software Zeiss Zen software (free download)
FIJI ImageJ (free download – 2D analysis)
▸ Xenogen IVIS Spectrum 200 (PM)
Model Xenogen IVIS Spectrum 200 (by Perkin Elmer)
Imaging modalities Bioluminescence (2D and 3D)
Fluorescence (2D and 3D)
Spectral imaging and unmixing
Filter sets 10 excitation filters covering 430nm to 750nm, 30nm bandwidth
18 emission filters covering 500nm to 850nm, 20nm bandwidth
Fields of View A: 3.9 cm (small dishes or tissues)
B: 6.5 cm (1 mouse)
C: 12.5 cm (3 mice)
D: 22.5 cm (5 mice)
Camera Andor iKon DZ436:
  • 2048 x 2048 pixels, with binning down to 256 x 256 for 64x sensitivity boost
  • Back-illuminated sensor, peak QE of 95%
  • Cooled to -80 deg C to eliminate thermal background counts, enabling up to 5min exposure time.
Advantages and techniques High-throughput in vivo imaging
Sensitive, non-invasive imaging of tumours
Software Living Image 4.5
▸ Leica SP8 Confocal and Multiphoton (Krembil)
Model Leica SP8 Confocal microscope
Leica DM8 physiological upright stand
Lasers, fluorophores Coherent Chameleon Discovery Laser
  • 2P/3P SHG/THG Imaging
  • Tunable beam 680-1300 nm
  • Fixed beam output 1040 nm
488nm (Alexa488, Cy2, FITC, GFP)
555nm (Alexa555, Alexa568, Alexa594, Cy3, DsRed, TxRed, RFP, mCherry)
Objective lenses HC-IRAPO 25X / 1.0 NA water dipping lens
Detectors 2 Internal detectors
  • 1 PMT
  • 1 HyD High efficiency detector
4 Nondescanned detectors
  • 2 PMT
  • 2 HyD High efficiency detectors
Filters Fully spectral, 400 to 700nm
Incubation Thermal plate
Advantages and techniques In vivo imaging
High-resolution confocal
High-speed resonant confocal
Multiphoton imaging for deep tissue penetration
Spectral unmixing
Second- and Third-harmonic generation imaging
Software Leica LAS-X (Free download)
FIJI ImageJ (free download – 2D analysis)
Imaris by Bitplane (licensed)
Huygens deconvolution (licensed)
Icon image of magnifying glass

Super-resolution

The best lateral resolution achievable on a standard confocal fluorescence microscope is about 200nm. The AOMF’s super-resolution microscopes can extend this down to 120nm (Airyscan), 50nm (STED), or even 20nm (GSD/STORM). Special sample preparation may be required, so consult with AOMF staff before preparing your samples. For 3D datasets, deconvolution can further improve the resolution.

confocal and sted images for superresolution
▸ Leica STED Confocal and Superresolution (PMCRT)
Model Leica TCS SP8 STED3X Confocal and Super-resolution microscope
Leica DMi8 CS inverted stand
Picoquant FLIM / FCS
Lasers, fluorophores 405nm (DAPI, Hoechst, Alexa405)
440nm (CFP)
White Light Laser (WLL), 475-675nm in 1nm steps (Alexa 488 to Cy5 and everything in between)
Objective lenses HC PL APO 10x/0.40 NA CS2
HC PL APO 20x/0.75 NA CS2
HC PL APO 63x/1.40 NA Oil immersion CS2
HC PL APO 63x/1.20 NA Water immersion CS2 motCorr (by request)
HC PL APO 93x/1.30 NA Glycerol immersion CS2 motCorr
HC PL APO 100x/1.40 NA Oil immersion CS2
Detectors 3 standard sensitivity PMT detectors + 2 HyD high-sensitivity detectors
Transmitted-light PMT
Filters Fully spectral, 400 to 700nm
Incubation Tokai Hit stage-top incubator
Advantages and techniques High-resolution confocal of fixed and live cells
STED super-resolution with 592nm, 660nm, and 775nm depletion lasers
Fluorescence Lifetime Imaging Microscopy (FLIM)
Fluorescence Correlation Spectroscopy (FCS)
Hyvolution 2 deconvolution
Spectral unmixing
Tiling / Stage Overview
AFC hardware autofocus
Software Leica LAS-X software (free download)
FIJI ImageJ (free download – 2D analysis)
Imaris by Bitplane (offline, licensed)
Huygens deconvolution (offline, licensed)
▸ Leica GSD / TIRF (TGH)
Model Leica SR GSD 3D
Leica DMi8 inverted Stand
Light sources Sola Light Engine LED for regular live cell imaging (DAPI, FITC, CY3, CY5 filters)
405 nm depletion laser for STORM/GSD super-resolution
488 nm laser (STORM/GSD/TIRF)
560nm laser (STORM/GSD/TIRF)
642nm laser (STORM/GSD/TIRF)
Objective lenses HC PL Apo 10x/0.45 NA
N PL 20x/0.40 NA PH1
HC PL Apo 20x/0.8 NA
HC PL Apo 40x/0.85 NA
HC PL Apo 100x/1.47 NA oil immersion, TIRF
HC PL Apo 160x/1.43 NA, oil immersion, GSD
Cameras Andor iXon Ultra 897 EMCCD
PCO Edge sCMOS
Incubation Tokai Hit stage-top incubator
Advantages and techniques STORM / GSD super-resolution:
  • Maximum resolution in X,Y: 20nm
  • Maximum resolution in Z: 50nm
  • SuMo stage minimizes drift
Total Internal Reflection Fluorescence (TIRF) microscopy
Live cell imaging
Software Leica LAS-X software
FIJI ImageJ (free download – 2D analysis)
▸ Zeiss LSM880 Confocal with Airyscan (Krembil)
Model Zeiss 880 Confocal with AiryScan
Zeiss AxioObserver 7 Stand
Lasers, fluorophores 405nm (DAPI, Hoechst, Alexa405)
488nm (Alexa488, Cy2, FITC, GFP)
555nm (Alexa555, Alexa568, Alexa594, Cy3, DsRed, TxRed, RFP, mCherry)
639nm (Alexa 647, Cy5)
Objective lenses Plan-Apochromat 10x/0.45 NA
Plan-Apochromat 20x/0.80 NA
Plan-Apochromat 40x/0.95 NA
Plan-Apochromat 63x/1.4 NA oil immersion
Detectors 2 standard sensitivity PMT detectors
1 high-sensitivity GaAsP detector
Filters Fully spectral, 400 to 700nm
Incubation Cell culture and 24-well plate format
Advantages and techniques High-resolution and extended resolution (AiryScan) confocal
Spectral unmixing
Live cell confocal imaging – FRET, FRAP
Software Zeiss Zen software (free download)
FIJI ImageJ (free download – 2D analysis)
Imaris by Bitplane (licensed)
Huygens deconvolution (licensed)
▸ Huygens Deconvolution – 1 license (PMCRT, Krembil)
Software Huygens Professional version 20.04
Modules include:
  • STED, confocal, multi-photon, widefield
  • GPU acceleration
  • PSF distiller
Description Deconvolution is an image restoration technique that uses mathematical algorithms to remove blur from an image, while at the same time reducing other degrading effects such as noise and aberrations. Huygens uses state-of-the-art algorithms including the Classic Maximum Likelihood Estimation (CLME) and Good’s Roughness Maximum Likelihood Estimation (GLME). Widefield, confocal, multi-photon, and STED images can all be deconvolved. A z-stack with optimized X-Y-Z sampling is required for deconvolution.
Icon image of analysis

Specialty instruments

In addition to confocal and widefield fluorescence microscopes, the AOMF is home to several specialty instruments. These include a Raman microscope (no, this has nothing to do with noodles), laser microdissection, and an automated Fluorescence In Situ Hybridization (FISH) system at our PMCRT site. Our TGH site has a Total Internal Reflection Fluorescence (TIRF) microscope for particularly thin optical sections adjacent to the coverslip, as well as a full cell culture suite. And our Krembil site sports a stereology system for rigorous cell counting (primarily for neuroscience).

graph image of Raman shift to Counts
▸ Renishaw Raman Microscope (PMCRT)
Model Renishaw inVia Confocal Raman Micro-spectrophotometer
Leica DMI 6000 inverted microscope stand
Light Sources Lasers for Raman:
  • 532nm (100mW)
  • 638nm (50mW)
  • 785mW (250mW)
Leica EL6000 metal halide fluorescence lamp
Objective lenses N Plan 2.5x / 0.05 NA (not suitable for Raman)
HCX PL FLUOTAR 5x / 0.15 NA
HC PLAN APO 20x / 0.70 NA
N Plan 20x / 0.45 NA (long working distance)
HCX PL APO 40x / 0.85 NA CORR
HCX PL APO 63x / 1.20 NA water immersion CORR
HCX APO 100x / 1.3 NA oil immersion (poor IR transmission)
Filter sets
  1. Reflected light
  2. DAPI
  3. GFP
  4. Cy3
  5. Cy5
Cameras RenCam CCD for spectroscopy (1024 x 256, deep depletion)
Lumenera 3-1M cooled monochrome CCD for fluorescence
Advantages and techniques Raman spectroscopy, both spatially resolved and in solutions
3 Excitation wavelengths
Raman mapping (low-res imaging)
Fluorescence/transmitted/reflected light contrasts for finding the specimen
Software Renishaw Wire 3.0
▸ MMI Laser Capture Microdissection (PMCRT)
Model MMI CellCut laser capture microdissection
Olympus IX81 inverted microscope stand
Light Source X-Cite 120 metal halide lamp (fluorescence)
100W halogen lamp (brightfield)
Objective lenses UPlanFL N 4x / 0.13 NA
UPlanFL N 10x / 0.3 NA Ph1
LUCPlanFL N 20x / 0.45 NA Ph2
LUCPlanFL N 40x / 0.60 NA Ph2
LUCPlanFL N 60x / 0.70 NA
Filter sets
  1. Brightfield (for H&E)
  2. DAPI
  3. GFP
  4. Cy3
Camera MMI CellCamera CXA285cF colour CCD
Advantages and techniques Laser Capture Microdissection of fixed slides for DNA/RNA sequencing.
Special membrane slides and collection caps are required.
Software MMI CellCut software
▸ Bioview FISH (PMCRT)
Model BioView Allegro Plus Automated FISH scanner
Olympus BX63 upright stand
Light Source X-Cite 120Q metal halide lamp
Objective lenses UPlan FL N 10x/0.3
UPlan SApo 20x/0.85 Oil
UPlan SApo 60x/0.35 Oil
Filter sets
  1. DAPI
  2. Aqua
  3. Green
  4. Gold
  5. Orange
  6. Red
  7. Cy5
Camera Dage-MTI XLMM CCD, 2048 x 2048
Advantages and techniques Automated FISH imaging and analysis (specialized setup required)
Software BioView Allegro
▸ Leica GSD / TIRF (TGH)
Model Leica SR GSD 3D
Leica DMi8 inverted Stand
Light sources Sola Light Engine LED for regular live cell imaging (DAPI, FITC, CY3, CY5 filters)
405 nm depletion laser for STORM/GSD super-resolution
488 nm laser (STORM/GSD/TIRF)
560nm laser (STORM/GSD/TIRF)
642nm laser (STORM/GSD/TIRF)
Objective lenses HC PL Apo 10x/0.45 NA
N PL 20x/0.40 NA PH1
HC PL Apo 20x/0.8 NA
HC PL Apo 40x/0.85 NA
HC PL Apo 100x/1.47 NA oil immersion, TIRF
HC PL Apo 160x/1.43 NA, oil immersion, GSD
Cameras Andor iXon Ultra 897 EMCCD
PCO Edge sCMOS
Incubation Tokai Hit stage-top incubator
Advantages and techniques STORM / GSD super-resolution:
  • Maximum resolution in X,Y: 20nm
  • Maximum resolution in Z: 50nm
  • SuMo stage minimizes drift
Total Internal Reflection Fluorescence (TIRF) microscopy
Live cell imaging
Software Leica LAS-X software
FIJI ImageJ (free download – 2D analysis)
▸ Cell culture suite (TGH)
Description Our TGH site has a fully equipped tissue culture lab, with a biosafety cabinet, incubators, cryogenic storage, centrifuge, 4 deg C fridge and -20 deg C freezer for sample storage. Users from off-site may request access to this equipment plus assistance from AOMF staff. Users generally provide their own consumables.
▸ MBF Stereology (Krembil)
Model Leica DMRB Stand
Light Sources X-Cite 120 metal halide lamp (fluorescence)
100W halogen lamp (brightfield)
Objective lenses HC Plan Fluotar 5x/0.15 NA
HC Plan Fluotar 10x/0.30 NA
Plan Fluotar 20x/0.50 NA
Plan Fluotar 40x/1.0 NA oil immersion
Plan Fluotar 63x/1.3 NA oil immersion
Filter sets
  1. DAPI
  2. FITC / Alexa488 / GFP
  3. Cy3 / Alexa 568
Camera Retiga 2000R Cooled Colour CCD
Advantages and techniques Stereological imaging and cell counting
Software MBF Stereo Investigator
FIJI ImageJ (free download – 2D analysis)
images for image analysis

Image analysis

Each site has at least one image analysis station with FIJI ImageJ for 2D analysis, Imaris (by Bitplane) for 3D rendering and quantification, and HALO (by Indica Labs) for whole-slide analysis of scanned tissue sections. Huygens Deconvolution software is available on analysis stations as well as directly on some of the confocal microscopes (one concurrent license). Instrument-specific software is also available, such as off-line versions of Nikon Elements, Zeiss Zen, Leica LAS-X, Xenogen Living Image, and more.

Icon image of a man sitting in front of computer
▸ IQ3 analysis station (PMCRT)
Description This analysis station has been temporarily removed due to COVID space restrictions. For Imaris please use IQ5.
▸ IQ4 analysis station (PMCRT)
Description This analysis station is dedicated to one of our 5 Halo licenses for whole-slide analysis of scanned brightfield or fluorescence tissue sections. Most slide formats are supported including:
  • Aperio (.svs)
  • Zeiss (.czi)
  • Nikon (.nd2)
  • Hamamatsu (.ndpi, .ndpis)
  • Leica (.scn, .lif)
  • Olympus (.vsi)
  • Perkin Elmer (.qptiff)
  • Ventana (.bif)
  • Non proprietary (.jpg, .tif)
Hardware HP Z840 desktop computer
Intel Xeon CPU E5-2623 v3 (3.00 GHz, 4 Cores, 8 Threads)
32GB RAM
Nvidia Quadro K620 GPU (384 CUDA cores)
HP Z30i 30” LED monitor (2560 x 1600)
Software Halo version 3.0311 (Indica Labs)
Aperio Imagescope version 12.3.2 (Leica)
▸ IQ5 analysis station (PMCRT)
Description This analysis station hosts one of our 5 Halo licenses for whole-slide analysis of scanned brightfield or fluorescence tissue sections. It can also be used for ImageJ (2D analysis), Huygens Professional (Deconvolution), Imaris (3D rendering and analysis) and Living Image (in vivo imaging analysis).
Hardware HP Z640 desktop computer
Intel Xeon CPU E5-2650 v4 (2.20 GHz, 12 Cores, 24 Threads)
32GB DDR4-2400 RAM
Nvidia Quadro M2000 GPU (768 CUDA cores, 4GB)
HP Z32x 31.5” LED monitor (3840 x 2160)
Software Halo version 3.0311 (Indica Labs)
Aperio Imagescope version 12.3.2 (Leica)
Imaris version 9.5 (Bitplane)
Huygens Professional version 20.04 deconvolution
Xenogen Living Image 4.5
FIJI ImageJ (2D analysis)
▸ IQ_PM (PM)
Description This analysis station hosts one of our 5 Halo licenses for whole-slide analysis of scanned brightfield or fluorescence tissue sections. It can also be used for ImageJ (2D analysis) and Volocity (3D rendering and analysis).
Hardware Dell Precision 7820 desktop computer
Dual Intel Xeon Silver 4112 (each CPU 2.6GHz, 4 Cores, 8 Threads)
64GB DDR4 RAM (2666MHz)
Nvidia Quadro RTX5000 GPU (3072 CUDA cores, 16GB)
Software Halo version 3.0311 (Indica Labs)
Aperio Imagescope version 12.3.2 (Leica)
Volocity
FIJI ImageJ (2D analysis)
▸ IQ_TGH (TGH)
Description This analysis station has a full version of Nikon Elements, as well Imaris (3D rendering and analysis)_ It can also be used for ImageJ (2D analysis) and Volocity (3D rendering and analysis).
Hardware HP Z620 desktop computer
Intel Xeon CPU E5-1650 v2 (3.5GHz, 6 Cores, 12 Threads)
64GB DDR4 RAM
Nvidia Quadro K2000 GPU (384 CUDA cores, 2GB)
Software Nikon Elements AR Analysis version 5.21.02
Imaris version 9.5.1 (Bitplane)
Hugyens Professional deconvolution
Volocity
FIJI ImageJ (2D analysis)
▸ IQ_WCIF (Krembil)
Description This analysis station hosts one of our 5 Halo licenses for whole-slide analysis of scanned brightfield or fluorescence tissue sections. It can also be used for ImageJ (2D analysis), Huygens Professional (Deconvolution), and Imaris (3D rendering and analysis).
Hardware Dell Precision 7810 desktop computer
Dual Intel Xeon CPU E5-2623 v3 (each CPU 3.0GHz, 4 Cores, 8 Threads)
128GB DDR4-2400 RAM
Nvidia Quadro M2000 GPU (768 CUDA cores, 4GB)
Software Halo version 3.0311 (Indica Labs)
Imaris version 9.5.1 (Bitplane)
Hugyens Professional deconvolution
FIJI ImageJ (2D analysis)
▸ HALO by Indica Labs – 5 licenses (PMCRT, PM, Krembil)
Description Halo is a powerful analysis platform for whole-slide analysis of scanned brightfield or fluorescence tissue sections. Most slide formats are supported including:
  • Aperio (.svs)
  • Zeiss (.czi)
  • Nikon (.nd2)
  • Hamamatsu (.ndpi, .ndpis)
  • Leica (.scn, .lif)
  • Olympus (.vsi)
  • Perkin Elmer (.qptiff)
  • Ventana (.bif)
  • Non proprietary (.jpg, .tif)
Our 5-seat license includes the following analysis modules:
  • AI Classifier
  • TMA analysis
  • Cytonuclear (brightfield and fluorescence)
  • Area quantitation (brightfield and fluorescence)
  • Highplex FL, Multiplex IHC
  • Object co-localization
  • Serial Section
  • Islet
  • Vacuole
  • ISH, FISH (RNAScope)
Software Halo version 3.0311 by Indica Labs
▸ Imaris by Bitplane – 3 licenses (PMCRT, TGH, Krembil)
Description Imaris is a powerful platform for visualization and analysis of 3D datasets, particularly confocal z-stacks and lightsheet volumes. Our 3 licenses include most of the available analysis modules including:
  • Core: 3D/4D rendering, detect objects, snapshots, animations
  • MeasurementPro: report and interact with detected objects
  • Coloc: true 3D co-localization
  • Vantage: statistical visualizations
  • TrackLineage: motion tracking in 2D and 3D
  • Filament tracer: trace neurons, vessels and more
  • Cell: segment and analyze cells and their compartments
  • XT: Matlab, Python, Java, R, ImageJ extensions
  • Batch: batch analysis using a saved protocol
Software Imaris version 9.6 by Bitplane (now Oxford Instruments)
▸ Huygens Deconvolution – 1 license (PMCRT, Krembil)
Description Deconvolution is an image restoration technique that uses mathematical algorithms to remove blur from an image, while at the same time reducing other degrading effects such as noise and aberrations. Huygens uses state-of-the-art algorithms including the Classic Maximum Likelihood Estimation (CLME) and Good’s Roughness Maximum Likelihood Estimation (GLME). Widefield, confocal, multi-photon, and STED images can all be deconvolved. A z-stack with optimized X-Y-Z sampling is required for deconvolution.
Software Huygens Professional version 20.04 Modules include:
  • STED, confocal, multi-photon, widefield
  • GPU acceleration
  • PSF distiller
▸ Aperio Imagescope (free download)

free download

▸ Zeiss Zen lite (free download)

free download

▸ Leica LAS-X (free download)

free download

▸ FIJI ImageJ (free download)

free download

Summary of fees

Service Type of Instrument UHN rate External Academic rate *
Training / Full Service Confocal / Multiphoton / Super-resolution $90/hr $100/hr
Regular usage
(unassisted)
Confocal / Multiphoton / Super-resolution $29 to $35/hr $35 to $40/hr
Full Service Whole-slide scanning: 20x brightfield (BF) $8/slide $10/slide
Full Service Whole-slide scanning: 20x fluorescence (FL) $12/slide $15/slide
Full Service Additional whole-slide scanning services for BF and FL: 40x, whole-mount slides, > 4 sections/slide, z-stacks
Training / Full Service Widefield $65/hr $75/hr
Regular usage
(unassisted)
Widefield $10 to $13/hr $12 to $16/hr
Training / Full Service Image analysis $65/hr $75/hr
Regular usage
(unassisted)
Image analysis $10/hr $12/hr
After Hours discount All instruments with permission - 20% - 20%
Overnight discount Live-cell imaging and batch image analysis - 50% - 50%

* Corporate rate is 2x External Academic rate

Expand Your Knowledge

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Instrument training courses

To protect the instruments and ensure optimum utilization, users must be trained by AOMF staff on each instrument before access will be granted. Our individual hands-on training sessions are 1 to 4 hours in length depending on the complexity of the instrument and the user’s prior experience. There is a maximum of 2 trainees per session (the 2nd receives a 50% discount). Contact AOMF staff for a free consultation to ensure that we set you up on the most appropriate instrument.

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Fundamentals of microscopy

This course is an excellent introduction for anyone who plans to get started with our high-end microscopes (confocal, multi-photon, super-resolution, etc.) but does not yet have fluorescence microscopy experience. You start by performing basic fluorescence microscopy and capturing an optimized multi-channel image. You will learn how to align the microscope for Koehler illumination and perform 4 transmitted-light contrast techniques: Brightfield, “Dirty Brightfield”, DIC and Phase Contrast. Finally, you will explore the 4 main elements of a good fluorescence microscope: lamps, filter sets, objective lenses, and cameras. Contact AOMF staff to book this one-on-one training session (groups of 2 are also permitted).

Prerequisite: Please watch this 40 min video before arriving for your course.

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Comprehensive Course on Fluorescence Microscopy

This week-long comprehensive course takes the student through all aspects of fluorescence microscopy using dynamic presentations (25%) and hands-on training and experience on the AOMF’s advanced microscopes (75%). Topics include: fundamentals of microscopy, contrast and resolution, confocal, spinning-disk confocal, two-photon, live-cell imaging, multi-channel timelapse acquisition, advanced confocal techniques (FRAP, FRET, spectral unmixing), super-resolution, image processing and quantitative analysis (calibrations, background corrections, noise removal, co-localization, deconvolution). The course includes 30hrs of microscope instruction, a course notebook with presentation slides and lab exercises, and refreshments and lunch each day.

Date: Due to COVID19, the 15th annual Comprehensive Course on Fluorescence Microscopy has not yet been announced.

Prerequisites: None, but it is expected that users have some basic biology/biomedical training.

Who should take this course? - Graduate students, technicians, research associates, and postdocs who require optical microscopy (particularly confocal) for their projects. Even if you already have used confocal extensively, this course will fill in the gaps in theoretical knowledge, help you to optimize your imaging, and teach you to get data from your images through careful image processing and analysis. - PI's: We have had a number of PI's take this course over the years, and they now have an excellent understanding of the limits of optical microscopy and what they can reasonably expect from their students and staff.

Course Outline:
  1. Day 1 – Fundamentals of Microscopy: how microscopes work, properties of light, contrast and resolution, widefield fluorescence microscopy, Phase Contrast, Differential Interference Contrast (DIC), Koehler illumination.
  2. Day 2 – Confocal: basic confocal imaging, optimizing channels, 3D Z-stacks, projections, Spinning Disk confocal, Two-Photon microscopy, measuring the Point Spread Function (PSF).
  3. Day 3 – Multidimensional Fluorescence Microscopy: multi-channel, multi-location, 3D, timelapse and live-cell imaging.
  4. Day 4 – Advanced Optical Microscopy: fast live-cell imaging, FRAP, FRET, TIRF, Super-Resolution (including STED, STORM, and SIM), spectral imaging, other advanced techniques and considerations in live cell imaging.
  5. Day 5 – Image Processing and Analysis: calibrations, filters, contrast enhancement, colocalization, deconvolution and digital pattern recognition. Note: On Friday, there are no afternoon lab sessions: the course ends after lunch.
Daily Schedule:
  • 09:00 – 10:15 am: Presentation (light refreshments provided)
  • 10:15 – 10:30 am: Break
  • 10:30 – 12:30 pm: Morning labs (3 students per microscope)
  • 12:30 – 01:30 pm: Lunch (provided)
  • 01:30 – 04:30 pm: Afternoon labs (3 students per microscope)

Cost: The course fee is $850 for UHN, $950 for academic external and $1,900 for industrial customers.

How to Apply: A registration form will be available here upon announcement of the next course.

Upon completion: Graduates of the course receive a non-accredited certificate.

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Optical Microscopy Users Group (O-MUG)

The Optical Microscopy Users Group meets once a month to discuss topics ranging from new microscopy systems to acquisition to analysis techniques. Each meeting comprises a 30-45min presentation on a selected topic followed by discussion. All levels of microscope users are welcome. Coffee is provided. NOTE: due to COVID19 these meetings are on hold.

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International Microscopy Visitors Program (IMVP)

The AOMF invites applicants from around the globe to participate in our International Microscopy Visitors Program (IMVP). The IMVP is a custom, self-paced program combining hands-on training by our expert staff with ample individual practice time on our microscopes for a truly thorough microscopy learning experience.

Suggested Duration: 3 to 10 days

Cost: $250/day per person

Each day will consist of 2hrs of hands-on microscope instruction time followed by 4hrs of unassisted microscope practise time. The program is designed for individuals or groups of no more than 4 participants (discounts for groups may apply). The IMVP can be arranged anytime of the year subject to microscope and staff availability.

The duration of the course is flexible, depending on your microscopy experience and ambitions. A 3-day program would be sufficient to gain a thorough working knowledge of confocal fluorescence microscopy, including:
  • using widefield (visual) mode to find your specimen
  • setting up lasers and detectors to suit your fluorescent labels
  • optimizing your confocal image intensity (laser powers, detector parameters, pinholes)
  • optimizing the number of pixels for publication-quality image sizes
  • adding DIC transmitted-light images to see cell and nuclear boundaries
  • creating confocal z-stacks and 3D projections
In a 5-day session we could preface the confocal training with the fundamentals of widefield microscopy, both transmitted-light and fluorescence, including such topics as:
  • following the lightpath to identify key components
  • transmitted-light contrasts (brightfield, DIC, Phase Contrast, and Darkfield)
  • fluorescence microscopy contrast (filtersets, lamps)
  • magnification, numerical aperture, and resolution
  • optimizing the microscope components
  • cameras and image acquisition
  • multi-channel fluorescence microscopy acquisition (eg: DAPI, FITC, Cy3, Cy5)
  • microscope care and maintenance
A longer visit could include such topics as:
  • advanced confocal and two-photon microscopy (FRAP, FRET, intravital imaging, second harmonic generation (SHG) imaging
  • live-cell microscopy
  • spinning-disk confocal microscopy

Please contact AOMF if you’re interested and we’d be happy to discuss the program with you!

Contact Us

PMCRT

The Princess Margaret Cancer Research Tower (PMCRT) in the MaRS Center is home to the largest and most comprehensive Optical Microscope Facility (AOMF) site.

15th floor, Room 15-305
PMCRT, 101 College St.
Toronto, ON, CANADA
M5G 1L7
Judy Cathcart (judy@aomf.ca) or Miria Bartolini (miria.bartolini@uhnresearch.ca)
Office: 416-581-8594
Lab: 416-634-8760

TGH

The Advanced Optical Microscopy Facility (AOMF)'s Toronto General Hospitals (TGH) site is well-equipped for both fixed and live cells, and designed for live-cell imaging.

MBRC 4th floor, Room??
Dr. Feng Xu (feng@aomf.ca)
Phone??

WCIF

The Bob and Joan Wright Cell Imaging Facility was established at the Toronto Western Hospital (now the Krembil Research Institute).

7th floor, Room 7KD-492
60 Leonard Ave,
Toronto, ON, CANADA
M5T 0S8

Dr. Kevin Conway (kevin.conway@uhnresearch.ca)
Tel: 647-705-2848

PM

The Optical Microscope Facility (AOMF)'s Princess Margaret Cancer Center is well-equipped for routine widefield and confocal microscopy.

? floor, Room?
Dr. Andrew Elia (andrew.elia@uhnresearch.ca)
Phone??

Questions?

AOMF, along with all other UHN Core facilities, can be accessed by any researcher, regardless of organization, through our Customer Management site (Stratocore PPMS) here. Create a free account to communicate directly with the facility and generate quotations for your work.

Please contact us for a free consultation to discuss your research needs with a member of our expert team. Meeting and discussing your research and goals is the best way for us to ensure the right technology and equipment is applied to your project.

Feel free to contact us for a free consultation and tour of the facility: we will gladly help you figure out what instruments and procedures you shhould use for your imaging experience. For a compelte list of equipment, click here.

Are you ready?

Our experienced staff can help you pick the exact instrument you need from our arsenal. To get the most out of our facilities, please contact us.

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