AOMF

The Advanced Optical Microscopy Facility
Accelerate your research by tapping into a world-class imaging facility

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

21

years of experience

Trusted by over

600

users a year

With over

40

instruments

Services

Get started by booking your free consultation

Free Consultations

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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

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Training and Support

  • Our individual hands-on training sessions are 1 to 4 hours in length, and cost $80 to $125/hr (see fee schedule).
  • Maximum 2 trainees per session.

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 $8.75/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

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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.

Instruments

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.

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
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

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).

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)

Instruments

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.

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
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
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

Summary of Fees

Service Type of Instrument UHN rate External Academic rate *
Training / Full Service Confocal / Multiphoton / Super-resolution $105/hr $130/hr
Regular usage (unassisted) Confocal / Multiphoton / Super-resolution $32 to $36/hr $38 to $43/hr
Full Service Whole-slide scanning: 20x brightfield (BF) $9/slide $12/slide
Full Service Whole-slide scanning: 20x fluorescence (FL) $15/slide $18/slide
Training / Full Service Widefield $85/hr $105/hr

* (Click for full fee schedule)

Courses

Instrument training courses

<p><span style="font-family: Roboto, sans-serif; font-size: 16px;">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.</span></p>

Sign Up

Fundamentals of microscopy

<p><span style="font-family: Roboto, sans-serif; font-size: 16px;">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).</span></p>

Sign Up

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 micro...

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 ex...

Optical Microscopy Users Group (O-MUG)

The Optical Microscopy Users Group meets several times per year 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. NOTE: these meetings have moved online - registration is free but required to participate live, and recordings will be made available when possible.

Webinar: BEYOND CONFOCAL MICROSCOPY

Speaker: 

James Jonkman, Staff Scientist
Advanced Optical Microscopy Facility (AOMF)
University Health Network, Toronto, Canada

Date: Feb 29th 2024 10 am EST

Event Details: Beyond Confocal Microscopy

Description: Confocal Microscopy is a standard tool for visualizing cells and tissues. But what if you want to go faster, deeper, or achieve higher resolution or wider fields of view? In this webinar, we reviewed some standard and advanced technologies and image analysis tools to help take your project to the next level.

Missed it?

Click here to watch the recording.

Resources


Good resources for learning about confocal fluorescence microscopy and related techniques:

It is helpful to have some background knowledge before jumping onto our sophisticated instruments:

Resources for helping me prepare my samples:

Trying to determine which dishes, fluorophores, antibodies, or fluorescent proteins to use? You may find these links useful. Nevertheless, you're welcome to discuss your planned sample prep with AOMF staff before purchasing reagents, dishes, etc. to make sure they are suitable for our microscopes. For your convenience, the AOMF stocks some coverslips and dishes in various sizes.

Team

James Jonkman

Staff Scientist & AOMF Manager

james.jonkman@uhn.ca

Judy Cathcart

Research Technician, PMCRT site Slide scanning, PMCRT instruments, safety

judith.cathcart@uhn.ca

Courtney McIntosh

Research Technician, PMCRT site Slide scanning, PMCRT instruments

courtney.mcintosh@uhn.ca

Feng Xu

Research Associate, TGH site TGH instruments, PM instruments, sample prep

xu.feng@uhn.ca

Contact Us

If you are based at one of our 4 sites, feel free to email a staff member at that site directly. Otherwise please contact aomf@uhnresearch.ca and we'll direct your inquiry appropriately.

AOMF - Princess Margaret Cancer Research Tower (PMCRT) site

The AOMF's largest site is in the MaRS Center in the Princess Margaret Cancer Research Tower (PMCRT). This site is equipped for slide scanning, confocal, multiphoton, widefield, super-resolution, and more.

Address:

101 College St., Room 15-305
Toronto, ON, CANADA, M5G 1L7

Sign Up

Our experienced staff can help you to choose the best instrument/technique for your application. We recommend that you contact us for a free consultation to discuss your project. When you're ready to start:

Questions?

The AOMF welcomes all users including corporate users, external academics, and of course internal (UHN) users. A variable fee schedule applies.

We recommend that you Contact Us for a free consultation to discuss your project. When you're ready to start: Review our Fee Schedule. Review our Policies regarding bookings, safety, and temporary COVID safety measures. This document is quite long, but we really do want you to read it before you start! Please follow the Getting Started Instructions for creating your new Stratocore account and accessing the AOMF calendars.

AOMF staff members are generally available Monday through Friday, 9am to 5pm. Experienced users are permitted After Hours access (24/7). Card access (arranged by AOMF staff) is required for all sites.

Please take a look at the resources section.