Imaging Facility

Updated August 15, 2018

The imaging facility is located in DV1074C and maintained by core facility technician, Xin Zhao, from department of biology under the supervision of VP research office and department of Biology. It functions as a shared research resource at UTM for optical microscopy, and is currently equipped with confocal and epi-fluorescence microscopes. In the future, we hope to enhance our imaging suite through the acquisition of new microscopes based on research requirements.


The facility can be accessed 24/7 via T-card – please contact Xin Zhao to obtain authorization. Xin Zhao is available Monday to Friday, 8:45am to 5pm.

Contact Information:

Xin Zhao
Core Facility Technician     
Department of Biology, Room DV4070
University of Toronto Mississauga
Tel:  905 569 4270

Facility Microscopes

Confocal Microscope, Zeiss LSM 800, Serial Number 2633000233

LSM800 is a laser scanning microscope system equipped with inverted fluorescence microscope, four laser lines, highly sensitive GaAsP detectors, Airscan detector and a transmitted light detector. It is capable of simultaneously acquiring 4 fluorescent images and 1 DIC image in a single sample scan, and able to do three dimensional fluorescence imaging. Airscan mode gives better signal-to-noise ratio.Technical specifications are as follows.


  • Observer. Z 1
  • High end fully motorized inverted microscope
  • Remote LCD touch screen allowing for remote control of all motorized components
  • Motorized Z motor with 10nm reproducibility and customizable variable speed focus control.
  • Motorized XY scanning stage, minimum travel range of 130x85mm, with <1um reproducibility.  Capable of holding slides, labtek chambers, 35mm dishes.
  • Motorized light path control, condensor, illumination shutters, reflector turret or filter cubes
  • Hardware based focus stabilization capable of being used for multiple xy locations in combination with z-stack, time course and spectral imaging in order to optimize acquisition from live cell experiments

Laser Scanning

  • Confocal
    • The confocal scan head should provide the following features at minimum;
      • XY image resolution of 6000x6000 pixels
      • Spectral detection with a spectral resolution as low as 1nm, with a range of 400-720nm (detection available >720)
      • Spectral un-mixing of up to 10 fluorophores, with 20 spectral channels
      • 360 degree rotation of scan field
      • Multi-Region of Interest FRAP capability, with ability to vary laser power between FRAP locations.
  • Optics
    • Top of the line microscopy optics for imaging of biomaterials and biological samples
      • EC Plan-Neofluar 10x/0.5 phase for overview imaging
      • Plan Apochromat 20x/0.8 NA objective for low magnification confocal imaging
      • Plan Apochromat 40x/1.4NA and Plan Apochromat 63x/1.4NA oil immersion for confocal imaging of coverslipped biological samples and live cell
      • Differential Interference Contrast optics for all imaging objectives
  • Lasers
    • Full complement of solid state lasers, with the following wavelengths and minimum powers, or equivalent.  Laser line intensity variable from 1-100% in 0.1% increments, with full linear response.

405nm (5mw)
488nm (10mw)
555nm (10mw)
639mw (5mw)

  • Detectors 
    • Capable of simultaneously acquiring 4 fluorescent images and 1 DIC image in a single sample scan.
    • Two internal high-sensitivity low noise Gallium Arsenide Phosphide detectors (GaAsP) and one high-sensitivity low noise super resolution detector (Airyscan).
    • Single transmitted light detector for DIC imaging in parallel with confocal.

Widefield Fluorescence 

  • Widefield fluorescence filters for DAPI, GFP, Cy3 and mCherry or equivalent dyes
  • Alignment-free extended long life (20000hr) LED fluorescence light source


Actively dampened isolation table


Windows 7 professional

Confocal Operating Software

Zen 2.3

Confocal Microscope, Zeiss LSM880, Serial number 2811000452

LSM880 is a laser scanning microscope system equipped with upright fluorescence microscope, four conventional laser lines and a tunable insight X3 laser for 2 photon imaging. It has GaAsP detectors, Airscan detector and Big 2 detector for 2 photon imaging. The system delivers super-resolution image and fast scanning speed, and is able to do three dimensional imaging.  2 photo imaging mode with specific long work distant objective is capable of requiring optical sections of deep tissue layers. Technical specifications are as follows.


  • Examiner. Z1
  • Upright
  • Objectives must be changed manually.
  • Z-Piezo stage is installed.
  • Objectives available
    1. EC PlnN 10X /0.3 DICI,  dry
    2. W Pln Apo 20x/ 1 w DICIII, water
    3. LD LCI plnApo 25x/0.8 W DICII, water /Glycerol with or without cover slip or oil with cover slip
    4. Pln Apo 63x/1.4 Oil DIC II, with cover slip

Laser Scanning

  • Laser lines available
    1. Diode 405-30 nm: Emission wavelength  410-513 nm
    2. Argon 458nm, 488nm , 514nm :  Emission wavelength 493- 604 nm
    3. DP55-561-10: Emission wavelength 566-633nm
    4. HeNe 633: Emission wavelength 638-755 nm
    5. InsightX3 Tunable: Excitation wavelength at 690-1080 nm, emission filters for Green at 500-550 nm and for Red at 575-610nm. It is designed for 2-photon imaging.
  • Detectors
    • Gallennium Arsenide Phosphide detectors (GaAsP)
    • One high-sensitivity low noise super resolution detector (Airyscan).
    • BiG-2 GaAsP Detector for 2 photon imaging

Wild field Fluorescence

  • Filter set available
  1. Dapi, Zeiss filter set 49, excitation at G365nm, emission at 445-450nm
  2. Alexa 488, Zeiss filter set 38, excitation BP 470/40, emission BP525/50
  3. Alexa 555, Zeiss Filter set 43, excitation BP 545/25, emission BP 605/70
  • Light source
    • X-cite 110LED

Air Table

Newport ST Series


Windows 7

Operating Software

Zen2.3 SP1

Confocal Microscope Spinning Disc, from Quorum Technologies.

The acquisition system is an X-Light V2 spinning disk confocal with an LDI-7 laser engine (both from 89 North) supplied and integrated by Quorum Technologies. The system is equipped with stage- top -live cell incubator for live cell imaging in 35 mm dish, 12 well, 24 well , 48 well and 96 well cell culture dishes. Confocal spinning disk technique is highly useful for high speed imaging of living cells expressing fluorescent proteins or stained with membrane-permeable synthetic dyes. Photo-bleaching and photo-toxicity are reduced with spinning disk microscopy. Technical specifications are as follows.

Laser line

The LDI-7 has seven laser lines.

Excitation wavelengths:

  • 405 nm
  • 445 nm
  • 470 nm
  • 520 nm
  • 528 nm
  • 555 nm
  • 640 nm

Emission filters:

  1. 460/50m
  2. 525/50m
  3. 610/75m
  4. 700/75m
  5. 528/640m (dual Green Red)
  6. 445/520m (dual CFP YFP)


Leica DMi8 inverted microscope with an ASI motorized stage.


The system is installed with two cameras, mounted via a twin-cam system. Both cameras are from Photometrics.

  1. Prime HS:  sCMOS camera, for high resolution.
  2. QuantEM:  EM-CCD, for high sensitivity applications.

Conventional Fluorescence  

The system also includes a conventional fluorescent light source, an X-Cite 110 LED from

Lumen Dynamics for reviewing samples by eye.
Four filter cubes are available (from Leica):

  1. Filter cube DAPI, material number 11525304
    • Excitation: 350/50
    • Emission 460/50
    • Dichroic: 400
  2. Filter cube Y5, size P, material number 11525312
    • Excitation: 620/60
    • Dichroic: 660
    • Emission: 700/75
  3. Filter cube FITC, material number 11525307
    • Excitation: 480/40
    • Dichroic: 505
    • Emission: 527/30
  4. Filter cube RHOD, material number 11525308
    • Excitation: 546/10
    • Dichroic: 560
    • Emission: 585/40

Live Cell incubation  

Accomplished with the Chamlide TC-W stage-top incubator. CO2 mixing is done with the FC-5N CO2/Air Mixer, also from LCI. CO2 level and temperature setting are adjustable.

Acquisition software

Metamorph v7.10 running on a Dell 7820, running Windows 10

Data Analysis Station

Equipped with a powerful computer (Windows 10) and imaging analysis software Volocity which is managed by network license server.

Epifluorescence Microscope  Nikon Eclipse 50i

It is a conventional fluorescence microscope, upright, for samples on slide with cover slip. 1X and 4X objectives are installed which are suit for low magnification requirement.




Phase contrast, NA 0.9, dry


  • Nikon Plan uw 1x/0.04
  • Nikon Plan Fluo 4x /0.13
  • Nikon Plan Fluo 10x/0.25
  • Nikon Plan  20x/0.04
  • Nikon Plan Fluo 100x1.30 Oil

Fluorescence Filters

  • ET Dapi
  • ET GFP
  • ET RsRed
  • UV-2A

Fluorescence power supply

  • X-Cite 120

Imaging Software

  • NIS-Elements BR3.0


Nikon DS-Ri1

Facility Services:

  • Free basic training on confocal microscopes is mandatory for new users.
  • Annual fee for internal user is applied. Please contact Xin Zhao for application form.
  • There is hourly usage fee for confocal microscopes. Internal user $25/hour, external user $40/hour.
  • A number of customized services such as sample fixation, antibody staining, and in-situ hybridization are available from core facility technician. Fees will be associated with some services, and the time commitment for such services will be discussed in advance with a cost of $ 30/ hour (plus the cost of materials) for technician’s time.  Please contact Xin Zhao for cost estimates and quotes.