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.

▸ 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	Coherent Chameleon Discovery Laser 2P/3P SHG/THG Imaging Tunable beam 680-1300 nm Fixed beam output 1040 nm 405nm (DAPI, Hoechst, Alexa405) 488nm (Alexa488, Cy2, FITC, GFP) 561nm (Alexa555, Alexa568, Alexa594, Cy3, DsRed, TxRed, RFP, mCherry) 633nm (Alexa 647, Cy5)
Objective lenses	FLUAR 5x/0.25 NA FLUAR 10x/0.50 NA W Plan-Apochromat 20x/1.0 NA water immersion Plan-Apochromat 63x/1.4 NA oil immersion
Detectors	3 standard PMT detectors 4-channel non-descanned (NDD) detector for deep imaging
Filters	Fully spectral, 400 to 700nm
Incubation	None
Advantages and techniques	In vivo imaging High-resolution confocal Multiphoton imaging for deep tissue penetration Spectral unmixing Second- and Third-harmonic generation imaging
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)

Whole-slide scanners

For tissue sections from 4um to 12um thick, AOMF staff will digitize your entire slide at high resolution starting at just 8.75/slide for brightfield and $15/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).

▸ 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	Copy the images you want to analyze to the local data drive, and add them to a Study (database) in HALO. 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. Regions of interest can also be defined with pen, negative pen (exclusion), or magnet tools. 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.

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.

▸ Zeiss AxioObserver Widefield (PMCRT)

Model	Zeiss AxioObserver.Z1 inverted stand
Light source	X-Cite 120Q metal halide fluorescence lamp
Filter sets	DAPI, Hoechst, Alexa405 (Chroma 39000 AT) Alexa488, Cy2, FITC, GFP (Chroma 49002 ET) Alexa555, Alexa568, Alexa594, Cy3, DsRed (Chroma 49004 ET) TexasRed, mCherry (Chroma 49008 ET) Alexa 647, Cy5 (Chroma 49019 ET longpass) CFP (Ex 436/10, Em 470LP) - available upon request YFP (Ex 500/20, Em 535/30) - available upon request 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 DAPI, Hoechst, Alexa405 (Chroma 49000 ET) Aqua, CFP (Chroma 49302) Alexa488, Cy2, FITC, GFP (Chroma 49303 ET) Gold, YFP (Chroma 49304 ET) Alexa555, Alexa568, Alexa594, Cy3, DsRed (Chroma 49305 ET) TexasRed, mCherry (Chroma 49306 ET) Alexa 647, Cy5 (Chroma 49009 ET narrow) FITC Longpass (Chroma 49012: Ex 480/40, Em 500LP) Cy3 Longpass (Chroma 49016: Ex 545/25, Em 570LP) Qdot Longpass (Ex 460SP, Em 500LP) - available upon request 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	DAPI, Hoechst, Alexa405 (Zeiss #49, Ex 365, Em 445/50) Alexa488, Cy2, FITC, GFP (Zeiss #38HE, Ex 470/40, Em 525/50) Alexa568, Alexa594, Cy3, DsRed, TxRed, mCherry (Chroma 49008) 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	Alexa488, Cy2, FITC, GFP (Ex 470/40, Em 500LP) 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	DAPI, Hoechst, Alexa405 Alexa488, Cy2, FITC, GFP Alexa555, Alexa568, Alexa594, Cy3, DsRed, TxRed, RFP, mCherry 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	DAPI, Hoechst, Alexa405 (Zeiss #49) CFP (Zeiss #47) Alexa488, Cy2, FITC, GFP (Zeiss #38 HE) Alexa555, Alexa568, Alexa594, Cy3, DsRed (Zeiss #20 HE) TexasRed, mCherry (Zeiss #45) 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	CFP Alexa488, Cy2, FITC, GFP Alexa568, Alexa594, Cy3, DsRed, TxRed, mCherry 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	DAPI, Hoechst, Alexa405 Alexa488, Cy2, FITC, GFP 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	DAPI, Hoechst, Alexa405 (Ex 340, Em 460/50) CFP, Cerulean (Ex 436/20, Em 470/24) Alexa488, Cy2, FITC, GFP (Ex 470/40, Em 525/50) YFP, Venus (Ex 500/20, Em 525/30) Alexa555, Alexa568, Alexa594, Cy3, DsRed (Ex 545/25, Em 605/70) TxRed, RFP, mCherry (Ex 560/40, Em 625/30) Alexa 647, Cy5 (Ex 640/30, Em 690/50) 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	DAPI, Hoechst, Alexa405 (Zeiss #49, Ex 365, Em 445/50) Alexa488, Cy2, FITC, GFP (Zeiss #38HE, Ex 470/40, Em 525/50) 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)

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.

▸ 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	Alexa488, Cy2, FITC, GFP (Ex 470/40, Em 500LP) 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	DAPI, Hoechst, Alexa405 (Zeiss #49, Ex 365, Em 445/50) Alexa488, Cy2, FITC, GFP (Zeiss #38HE, Ex 470/40, Em 525/50) Alexa568, Alexa594, Cy3, DsRed, TxRed, mCherry (Chroma 49008) 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)

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.

▸ 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.

High-Multiplex Tissue Imaging

Standard immunofluorescence microscopy (both widefield and confocal) allows one to image 4 colours sequentially without significant spectral overlap. High-multiplex imaging systems go beyond this practical limit to visualize 6, 8, or even up to 40 labeled antibodies in a single tissue slice. The Hyperion Imaging Mass Cytometer (IMC) replaces fluorescent tags with up to 40 metal isotopes: a pulsed laser in the IMC ablates 1um-diameter spots across the tissue which are then analyzed with time-of-flight (TOF) mass spectrometry. Imaging Mass Cytometry is therefore an extremely powerful technique for studying complex cellular processes and interactions at the intact tissue level.

▸ Hyperion Imaging Mass Cytometer (PMCRT)

Model	Fluidigm Hyperion Imaging System, comprising: Hyperion Tissue Imager Helios mass cytometer
Channels	135
Frequency	200 pixels / s
Detection limit	≥ 400 copies per um2
Wet tissue thickness for full ablation	≤ 7 um
Addressable sample size on slide	≥ 15mm x 45mm
Optical view of sample	≥ 250um x 250um
File type	.mcd, OME-TIFF, Multipage TIFF, .txt
Scan area	≥ 1mm2 / 2hr (@ 200 Hz)
Advantages and techniques	High-multiplex imaging of tissues sections
Software	MCD viewer (free download) FIJI ImageJ (free download) Cell Profiler (free download) Halo (Indica Labs)

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).

▸ 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	Reflected light DAPI GFP Cy3 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	Brightfield (for H&E) DAPI GFP 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	DAPI Aqua Green Gold Orange Red 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	DAPI FITC / Alexa488 / GFP 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)

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.

▸ 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

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. 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.

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