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

17

years of exeperience

Trusted by over

600

users a year

With over

40

instruments

Services

Get started by booking your free consultation

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.

Services

Get started by booking your free consultation

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

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 and widefield images
▸ Zeiss LSM700 Confocal (PMCRT)
  • Full exons and flanking regions for known to be involved in cancer and its clinical management
  • full length (exons and introns) of 3 genes, BRCA1, BRCA2 and MLH1, and an upstream promoter region of TERT, in order to aid in the detection of large deletions or duplications in these genes which are known to cause inherited cancers.
Platform: Illumina NextSeq 500
Input: 250ng DNA; KAPA Input: 100ng DNA
▸ Zeiss LSM710 Confocal and Multiphoton (PMCRT)
  • Full exons and flanking regions for known to be involved in cancer and its clinical management
  • full length (exons and introns) of 3 genes, BRCA1, BRCA2 and MLH1, and an upstream promoter region of TERT, in order to aid in the detection of large deletions or duplications in these genes which are known to cause inherited cancers.
Platform: Illumina NextSeq 500
Input: 250ng DNA; KAPA Input: 100ng DNA
▸ Leica SP8 Confocal (PMCRT)
  • Full exons and flanking regions for known to be involved in cancer and its clinical management
  • full length (exons and introns) of 3 genes, BRCA1, BRCA2 and MLH1, and an upstream promoter region of TERT, in order to aid in the detection of large deletions or duplications in these genes which are known to cause inherited cancers.
Platform: Illumina NextSeq 500
Input: 250ng DNA; KAPA Input: 100ng DNA
▸ Leica STED Confocal and Superresolution (PMCRT)
  • Full exons and flanking regions for known to be involved in cancer and its clinical management
  • full length (exons and introns) of 3 genes, BRCA1, BRCA2 and MLH1, and an upstream promoter region of TERT, in order to aid in the detection of large deletions or duplications in these genes which are known to cause inherited cancers.
Platform: Illumina NextSeq 500
Input: 250ng DNA; KAPA Input: 100ng DNA
▸ Nikon A1R Confocal (TGH)
  • Full exons and flanking regions for known to be involved in cancer and its clinical management
  • full length (exons and introns) of 3 genes, BRCA1, BRCA2 and MLH1, and an upstream promoter region of TERT, in order to aid in the detection of large deletions or duplications in these genes which are known to cause inherited cancers.
Platform: Illumina NextSeq 500
Input: 250ng DNA; KAPA Input: 100ng DNA
▸ Olympus FV1000_A Confocal (TGH)
  • Full exons and flanking regions for known to be involved in cancer and its clinical management
  • full length (exons and introns) of 3 genes, BRCA1, BRCA2 and MLH1, and an upstream promoter region of TERT, in order to aid in the detection of large deletions or duplications in these genes which are known to cause inherited cancers.
Platform: Illumina NextSeq 500
Input: 250ng DNA; KAPA Input: 100ng DNA
▸ Olympus FV1000_B Confocal (TGH)
  • Full exons and flanking regions for known to be involved in cancer and its clinical management
  • full length (exons and introns) of 3 genes, BRCA1, BRCA2 and MLH1, and an upstream promoter region of TERT, in order to aid in the detection of large deletions or duplications in these genes which are known to cause inherited cancers.
Platform: Illumina NextSeq 500
Input: 250ng DNA; KAPA Input: 100ng DNA
▸ WaveFX Spinning-disk Confocal (TGH)
  • Full exons and flanking regions for known to be involved in cancer and its clinical management
  • full length (exons and introns) of 3 genes, BRCA1, BRCA2 and MLH1, and an upstream promoter region of TERT, in order to aid in the detection of large deletions or duplications in these genes which are known to cause inherited cancers.
Platform: Illumina NextSeq 500
Input: 250ng DNA; KAPA Input: 100ng DNA
▸ Olympus FV1000_C Confocal (PM)
  • Full exons and flanking regions for known to be involved in cancer and its clinical management
  • full length (exons and introns) of 3 genes, BRCA1, BRCA2 and MLH1, and an upstream promoter region of TERT, in order to aid in the detection of large deletions or duplications in these genes which are known to cause inherited cancers.
Platform: Illumina NextSeq 500
Input: 250ng DNA; KAPA Input: 100ng DNA
▸ WaveFX Spinning-disk Confocal (PM)
  • Full exons and flanking regions for known to be involved in cancer and its clinical management
  • full length (exons and introns) of 3 genes, BRCA1, BRCA2 and MLH1, and an upstream promoter region of TERT, in order to aid in the detection of large deletions or duplications in these genes which are known to cause inherited cancers.
Platform: Illumina NextSeq 500
Input: 250ng DNA; KAPA Input: 100ng DNA
▸ Zeiss LSM880 Confocal with Airyscan (Krembil)
  • Full exons and flanking regions for 52 hereditary cancer genes and 9 non-cancer genes
Platform: Illumina NextSeq 500 or MiSeq
Input: 250ng DNA
▸ Leica SP8 Confocal and Multiphoton (Krembil)
  • Cell free DNA (cfDNA) isolated from plasma enables a non-invasive and cost-effective alternative to traditional biopsy samples
cfDNA input: 20ng
Panel: commercially available (ThermoFisher)

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)
  • Full exons and flanking regions for known to be involved in cancer and its clinical management
  • full length (exons and introns) of 3 genes, BRCA1, BRCA2 and MLH1, and an upstream promoter region of TERT, in order to aid in the detection of large deletions or duplications in these genes which are known to cause inherited cancers.
Platform: Illumina NextSeq 500
Input: 250ng DNA; KAPA Input: 100ng DNA
▸ Zeiss AxioScan fluorescence scanner (PMCRT, drop-box at Krembil)
  • Full exons and flanking regions for known to be involved in cancer and its clinical management
  • full length (exons and introns) of 3 genes, BRCA1, BRCA2 and MLH1, and an upstream promoter region of TERT, in order to aid in the detection of large deletions or duplications in these genes which are known to cause inherited cancers.
Platform: Illumina NextSeq 500
Input: 250ng DNA; KAPA Input: 100ng DNA
▸ HALO whole-slide analysis software (PMCRT, PM, and Krembil)
  • Full exons and flanking regions for known to be involved in cancer and its clinical management
  • full length (exons and introns) of 3 genes, BRCA1, BRCA2 and MLH1, and an upstream promoter region of TERT, in order to aid in the detection of large deletions or duplications in these genes which are known to cause inherited cancers.
Platform: Illumina NextSeq 500
Input: 250ng DNA; KAPA Input: 100ng DNA

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 image
▸ Zeiss AxioObserver Widefield (PMCRT)
  • Full exons and flanking regions for known to be involved in cancer and its clinical management
  • full length (exons and introns) of 3 genes, BRCA1, BRCA2 and MLH1, and an upstream promoter region of TERT, in order to aid in the detection of large deletions or duplications in these genes which are known to cause inherited cancers.
Platform: Illumina NextSeq 500
Input: 250ng DNA; KAPA Input: 100ng DNA
▸ Zeiss AxioImager Widefield (PMCRT)
  • Full exons and flanking regions for known to be involved in cancer and its clinical management
  • full length (exons and introns) of 3 genes, BRCA1, BRCA2 and MLH1, and an upstream promoter region of TERT, in order to aid in the detection of large deletions or duplications in these genes which are known to cause inherited cancers.
Platform: Illumina NextSeq 500
Input: 250ng DNA; KAPA Input: 100ng DNA
▸ Zeiss AxioZoom Macroscope (PMCRT)
  • Full exons and flanking regions for known to be involved in cancer and its clinical management
  • full length (exons and introns) of 3 genes, BRCA1, BRCA2 and MLH1, and an upstream promoter region of TERT, in order to aid in the detection of large deletions or duplications in these genes which are known to cause inherited cancers.
Platform: Illumina NextSeq 500
Input: 250ng DNA; KAPA Input: 100ng DNA
▸ Olympus BX51 Widefield (PMCRT)
  • Full exons and flanking regions for known to be involved in cancer and its clinical management
  • full length (exons and introns) of 3 genes, BRCA1, BRCA2 and MLH1, and an upstream promoter region of TERT, in order to aid in the detection of large deletions or duplications in these genes which are known to cause inherited cancers.
Platform: Illumina NextSeq 500
Input: 250ng DNA; KAPA Input: 100ng DNA
▸ Leica Stereomicroscope (PMCRT)
  • Full exons and flanking regions for known to be involved in cancer and its clinical management
  • full length (exons and introns) of 3 genes, BRCA1, BRCA2 and MLH1, and an upstream promoter region of TERT, in order to aid in the detection of large deletions or duplications in these genes which are known to cause inherited cancers.
Platform: Illumina NextSeq 500
Input: 250ng DNA; KAPA Input: 100ng DNA
▸ Zeiss AxioObserver_TGH Widefield (TGH)
  • Full exons and flanking regions for known to be involved in cancer and its clinical management
  • full length (exons and introns) of 3 genes, BRCA1, BRCA2 and MLH1, and an upstream promoter region of TERT, in order to aid in the detection of large deletions or duplications in these genes which are known to cause inherited cancers.
Platform: Illumina NextSeq 500
Input: 250ng DNA; KAPA Input: 100ng DNA
▸ Zeiss AxioImager_PM Widefield (PM)
  • Full exons and flanking regions for known to be involved in cancer and its clinical management
  • full length (exons and introns) of 3 genes, BRCA1, BRCA2 and MLH1, and an upstream promoter region of TERT, in order to aid in the detection of large deletions or duplications in these genes which are known to cause inherited cancers.
Platform: Illumina NextSeq 500
Input: 250ng DNA; KAPA Input: 100ng DNA
▸ Leica Stereomicroscope_PM (PM)
  • Full exons and flanking regions for known to be involved in cancer and its clinical management
  • full length (exons and introns) of 3 genes, BRCA1, BRCA2 and MLH1, and an upstream promoter region of TERT, in order to aid in the detection of large deletions or duplications in these genes which are known to cause inherited cancers.
Platform: Illumina NextSeq 500
Input: 250ng DNA; KAPA Input: 100ng DNA
▸ Leica DMI Widefield (PM)
  • Full exons and flanking regions for known to be involved in cancer and its clinical management
  • full length (exons and introns) of 3 genes, BRCA1, BRCA2 and MLH1, and an upstream promoter region of TERT, in order to aid in the detection of large deletions or duplications in these genes which are known to cause inherited cancers.
Platform: Illumina NextSeq 500
Input: 250ng DNA; KAPA Input: 100ng DNA
▸ Zeiss AxioObserver_WCIF Widefield (Krembil)
  • Full exons and flanking regions for known to be involved in cancer and its clinical management
  • full length (exons and introns) of 3 genes, BRCA1, BRCA2 and MLH1, and an upstream promoter region of TERT, in order to aid in the detection of large deletions or duplications in these genes which are known to cause inherited cancers.
Platform: Illumina NextSeq 500
Input: 250ng DNA; KAPA Input: 100ng DNA
▸ Zeiss AxioZoom_WCIF Macroscope (Krembil)
  • Full exons and flanking regions for 52 hereditary cancer genes and 9 non-cancer genes
Platform: Illumina NextSeq 500 or MiSeq
Input: 250ng DNA

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)
  • Full exons and flanking regions for known to be involved in cancer and its clinical management
  • full length (exons and introns) of 3 genes, BRCA1, BRCA2 and MLH1, and an upstream promoter region of TERT, in order to aid in the detection of large deletions or duplications in these genes which are known to cause inherited cancers.
Platform: Illumina NextSeq 500
Input: 250ng DNA; KAPA Input: 100ng DNA
▸ Leica Stereomicroscope (PMCRT)
  • Full exons and flanking regions for known to be involved in cancer and its clinical management
  • full length (exons and introns) of 3 genes, BRCA1, BRCA2 and MLH1, and an upstream promoter region of TERT, in order to aid in the detection of large deletions or duplications in these genes which are known to cause inherited cancers.
Platform: Illumina NextSeq 500
Input: 250ng DNA; KAPA Input: 100ng DNA
▸ Zeiss AxioZoom Macroscope (PMCRT)
  • Full exons and flanking regions for known to be involved in cancer and its clinical management
  • full length (exons and introns) of 3 genes, BRCA1, BRCA2 and MLH1, and an upstream promoter region of TERT, in order to aid in the detection of large deletions or duplications in these genes which are known to cause inherited cancers.
Platform: Illumina NextSeq 500
Input: 250ng DNA; KAPA Input: 100ng DNA
▸ Xenogen IVIS Spectrum 200 (PM)
  • Full exons and flanking regions for known to be involved in cancer and its clinical management
  • full length (exons and introns) of 3 genes, BRCA1, BRCA2 and MLH1, and an upstream promoter region of TERT, in order to aid in the detection of large deletions or duplications in these genes which are known to cause inherited cancers.
Platform: Illumina NextSeq 500
Input: 250ng DNA; KAPA Input: 100ng DNA
▸ Leica SP8 Confocal and Multiphoton (Krembil)
  • Full exons and flanking regions for known to be involved in cancer and its clinical management
  • full length (exons and introns) of 3 genes, BRCA1, BRCA2 and MLH1, and an upstream promoter region of TERT, in order to aid in the detection of large deletions or duplications in these genes which are known to cause inherited cancers.
Platform: Illumina NextSeq 500
Input: 250ng DNA; KAPA Input: 100ng DNA

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)
  • Full exons and flanking regions for known to be involved in cancer and its clinical management
  • full length (exons and introns) of 3 genes, BRCA1, BRCA2 and MLH1, and an upstream promoter region of TERT, in order to aid in the detection of large deletions or duplications in these genes which are known to cause inherited cancers.
Platform: Illumina NextSeq 500
Input: 250ng DNA; KAPA Input: 100ng DNA
▸ Leica GSD / TIRF (TGH)
  • Full exons and flanking regions for known to be involved in cancer and its clinical management
  • full length (exons and introns) of 3 genes, BRCA1, BRCA2 and MLH1, and an upstream promoter region of TERT, in order to aid in the detection of large deletions or duplications in these genes which are known to cause inherited cancers.
Platform: Illumina NextSeq 500
Input: 250ng DNA; KAPA Input: 100ng DNA
▸ Zeiss LSM880 Confocal with Airyscan (Krembil)
  • Full exons and flanking regions for known to be involved in cancer and its clinical management
  • full length (exons and introns) of 3 genes, BRCA1, BRCA2 and MLH1, and an upstream promoter region of TERT, in order to aid in the detection of large deletions or duplications in these genes which are known to cause inherited cancers.
Platform: Illumina NextSeq 500
Input: 250ng DNA; KAPA Input: 100ng DNA
▸ Huygens Deconvolution – 1 license (PMCRT, Krembil)
  • Full exons and flanking regions for known to be involved in cancer and its clinical management
  • full length (exons and introns) of 3 genes, BRCA1, BRCA2 and MLH1, and an upstream promoter region of TERT, in order to aid in the detection of large deletions or duplications in these genes which are known to cause inherited cancers.
Platform: Illumina NextSeq 500
Input: 250ng DNA; KAPA Input: 100ng DNA

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)
  • Full exons and flanking regions for known to be involved in cancer and its clinical management
  • full length (exons and introns) of 3 genes, BRCA1, BRCA2 and MLH1, and an upstream promoter region of TERT, in order to aid in the detection of large deletions or duplications in these genes which are known to cause inherited cancers.
Platform: Illumina NextSeq 500
Input: 250ng DNA; KAPA Input: 100ng DNA
▸ MMI Laser Capture Microdissection (PMCRT)
  • Full exons and flanking regions for known to be involved in cancer and its clinical management
  • full length (exons and introns) of 3 genes, BRCA1, BRCA2 and MLH1, and an upstream promoter region of TERT, in order to aid in the detection of large deletions or duplications in these genes which are known to cause inherited cancers.
Platform: Illumina NextSeq 500
Input: 250ng DNA; KAPA Input: 100ng DNA
▸ Bioview FISH (PMCRT)
  • Full exons and flanking regions for known to be involved in cancer and its clinical management
  • full length (exons and introns) of 3 genes, BRCA1, BRCA2 and MLH1, and an upstream promoter region of TERT, in order to aid in the detection of large deletions or duplications in these genes which are known to cause inherited cancers.
Platform: Illumina NextSeq 500
Input: 250ng DNA; KAPA Input: 100ng DNA
▸ Leica GSD / TIRF (TGH)
  • Full exons and flanking regions for known to be involved in cancer and its clinical management
  • full length (exons and introns) of 3 genes, BRCA1, BRCA2 and MLH1, and an upstream promoter region of TERT, in order to aid in the detection of large deletions or duplications in these genes which are known to cause inherited cancers.
Platform: Illumina NextSeq 500
Input: 250ng DNA; KAPA Input: 100ng DNA
▸ Cell culture suite (TGH)
  • Full exons and flanking regions for known to be involved in cancer and its clinical management
  • full length (exons and introns) of 3 genes, BRCA1, BRCA2 and MLH1, and an upstream promoter region of TERT, in order to aid in the detection of large deletions or duplications in these genes which are known to cause inherited cancers.
Platform: Illumina NextSeq 500
Input: 250ng DNA; KAPA Input: 100ng DNA
▸ MBF Stereology (Krembil)
  • Full exons and flanking regions for known to be involved in cancer and its clinical management
  • full length (exons and introns) of 3 genes, BRCA1, BRCA2 and MLH1, and an upstream promoter region of TERT, in order to aid in the detection of large deletions or duplications in these genes which are known to cause inherited cancers.
Platform: Illumina NextSeq 500
Input: 250ng DNA; KAPA Input: 100ng DNA
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.

▸ IQ3 analysis station (PMCRT)
  • Full exons and flanking regions for known to be involved in cancer and its clinical management
  • full length (exons and introns) of 3 genes, BRCA1, BRCA2 and MLH1, and an upstream promoter region of TERT, in order to aid in the detection of large deletions or duplications in these genes which are known to cause inherited cancers.
Platform: Illumina NextSeq 500
Input: 250ng DNA; KAPA Input: 100ng DNA
▸ IQ4 analysis station (PMCRT)
  • Full exons and flanking regions for known to be involved in cancer and its clinical management
  • full length (exons and introns) of 3 genes, BRCA1, BRCA2 and MLH1, and an upstream promoter region of TERT, in order to aid in the detection of large deletions or duplications in these genes which are known to cause inherited cancers.
Platform: Illumina NextSeq 500
Input: 250ng DNA; KAPA Input: 100ng DNA
▸ IQ5 analysis station (PMCRT)
  • Full exons and flanking regions for known to be involved in cancer and its clinical management
  • full length (exons and introns) of 3 genes, BRCA1, BRCA2 and MLH1, and an upstream promoter region of TERT, in order to aid in the detection of large deletions or duplications in these genes which are known to cause inherited cancers.
Platform: Illumina NextSeq 500
Input: 250ng DNA; KAPA Input: 100ng DNA
▸ IQ_PM (PM)
  • Full exons and flanking regions for known to be involved in cancer and its clinical management
  • full length (exons and introns) of 3 genes, BRCA1, BRCA2 and MLH1, and an upstream promoter region of TERT, in order to aid in the detection of large deletions or duplications in these genes which are known to cause inherited cancers.
Platform: Illumina NextSeq 500
Input: 250ng DNA; KAPA Input: 100ng DNA
▸ IQ_TGH (TGH)
  • Full exons and flanking regions for known to be involved in cancer and its clinical management
  • full length (exons and introns) of 3 genes, BRCA1, BRCA2 and MLH1, and an upstream promoter region of TERT, in order to aid in the detection of large deletions or duplications in these genes which are known to cause inherited cancers.
Platform: Illumina NextSeq 500
Input: 250ng DNA; KAPA Input: 100ng DNA
▸ IQ_WCIF (Krembil)
  • Full exons and flanking regions for known to be involved in cancer and its clinical management
  • full length (exons and introns) of 3 genes, BRCA1, BRCA2 and MLH1, and an upstream promoter region of TERT, in order to aid in the detection of large deletions or duplications in these genes which are known to cause inherited cancers.
Platform: Illumina NextSeq 500
Input: 250ng DNA; KAPA Input: 100ng DNA
▸ HALO by Indica Labs – 5 licenses (PMCRT, PM, Krembil)
  • Full exons and flanking regions for known to be involved in cancer and its clinical management
  • full length (exons and introns) of 3 genes, BRCA1, BRCA2 and MLH1, and an upstream promoter region of TERT, in order to aid in the detection of large deletions or duplications in these genes which are known to cause inherited cancers.
Platform: Illumina NextSeq 500
Input: 250ng DNA; KAPA Input: 100ng DNA
▸ Imaris by Bitplane – 3 licenses (PMCRT, TGH, Krembil)
  • Full exons and flanking regions for known to be involved in cancer and its clinical management
  • full length (exons and introns) of 3 genes, BRCA1, BRCA2 and MLH1, and an upstream promoter region of TERT, in order to aid in the detection of large deletions or duplications in these genes which are known to cause inherited cancers.
Platform: Illumina NextSeq 500
Input: 250ng DNA; KAPA Input: 100ng DNA
▸ Huygens Deconvolution – 1 license (PMCRT, Krembil)
  • Full exons and flanking regions for known to be involved in cancer and its clinical management
  • full length (exons and introns) of 3 genes, BRCA1, BRCA2 and MLH1, and an upstream promoter region of TERT, in order to aid in the detection of large deletions or duplications in these genes which are known to cause inherited cancers.
Platform: Illumina NextSeq 500
Input: 250ng DNA; KAPA Input: 100ng DNA
▸ Aperio Imagescope (free download)
  • Full exons and flanking regions for known to be involved in cancer and its clinical management
  • full length (exons and introns) of 3 genes, BRCA1, BRCA2 and MLH1, and an upstream promoter region of TERT, in order to aid in the detection of large deletions or duplications in these genes which are known to cause inherited cancers.
Platform: Illumina NextSeq 500
Input: 250ng DNA; KAPA Input: 100ng DNA
▸ Zeiss Zen lite (free download)
  • Full exons and flanking regions for 52 hereditary cancer genes and 9 non-cancer genes
Platform: Illumina NextSeq 500 or MiSeq
Input: 250ng DNA
▸ FIJI ImageJ (free download)
  • Cell free DNA (cfDNA) isolated from plasma enables a non-invasive and cost-effective alternative to traditional biopsy samples
cfDNA input: 20ng
Panel: commercially available (ThermoFisher)

Fee Table

Service Instruments Internal (Hourly) External Academic
(Hourly)
External Corporate
(Hourly)
Flow Analysis
(unaided)
BD FACS Canto II $30.00 $30.00 $60.00
Flow Analysis
(unaided)
BD Fortessa1, BD Fortessa2, BD Fortessa X20 $40.00 $40.00 $80.00
Flow Analysis
(unaided)
Cytoflex $40.00 $40.00 $80.00
Cell sorting
(peak hours)
BD Fusion, Astrios 1, Astrios2, Astrios3 $75.00 $75.00 $150.00
Cell sorting
(after hours)
BD Fusion, Astrios1, Astrios2, Astrios3 $112.50 $112.50 $225.00
Assisted acquisition, training
(peak hours)
All instruments $75.00 $75.00 $150.00

Expand Your Knowledge

Instrument training courses

Processing and extraction along with CAP/CLIA sample banking.

Panels currently validated and available:

LSC17 assay: Custom 17 gene panel for stratifying acute myeloid leukemia (AML) patients for their level of relapse risk. Read more about it here.
Platform: NanoString, 17 genes
Technology: gene expression

Fundamentals of microscopy

NanoString technology enables the direct detection of RNA, DNA or protein in a sample using patented molecular barcodes and a unique hybridization and detection platform.

Panels currently validated and available:

LSC17 assay: Custom 17 gene panel for stratifying acute myeloid leukemia (AML) patients for their level of relapse risk. Read more about it here.
Platform: NanoString, 17 genes
Technology: gene expression

Comprehensive Course on Fluorescence Microscopy

ddPCR Enables the quantitation of nucleic acids in a sample using a miniaturized PCR procedure that is executed in a high-throughput manner

  • enables the detection of potentially relevant variants at frequencies as low as 0.5%
  • Somatically acquired variants that affect patient management can sometimes occur at frequencies less than ten percent (10%), which are difficult to detect by Sanger sequencing or other standard laboratory assays
  • Commercially available probe sets
Platform: BioRad QX200

Optical Microscopy Users Group (O-MUG)

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.

Panels currently validated and available:

LSC17 assay: Custom 17 gene panel for stratifying acute myeloid leukemia (AML) patients for their level of relapse risk. Read more about it here.
Platform: NanoString, 17 genes
Technology: gene expression

Super-resolution workshop

Design advice for your clinical research assay and validation and testing according to CAP/CLIA guidelines

Contact us for more details

International Microscopy Visitors Program (IMVP)

Design advice for your clinical research assay and validation and testing according to CAP/CLIA guidelines

Contact us for more details

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.

PMCRT: 15th floor, Room 15-305
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.

TGH: 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).

WCIF: TWH 7th floor, Room?
Dr. Kevin Conway (kevin.conway@uhnresearch.ca)
Phone: 647-705-2848

PM

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

PM: ? 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.
Sign Up

© date University Health Network