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Light Microscopy

Light Microscopy Core

Located on the 5th floor in the Life Science Laboratories the Light Microscopy facility provides powerful resources for imaging model organisms, tissue, cells, biomaterials, and artificial structures and houses state-of-the-art equipment including almost every light microscopy imaging modality currently available. Cell culture facilities are also available as well as other routine needs for biological imaging. This facility is one of a few designated Nikon Centers of Excellence providing a unique opportunity for training, demonstration, instrument development, and research.

The facility accepts samples and will perform requested analysis. We offer training to users to conduct experimentation for use on a fee for service basis to both internal and external researchers, academic or industry based. Following an initial consultation, covering experimental parameters training and access is arranged through the director.

Industry Sponsorship
The benefits of working with Nikon as an industry collaborator are that UMass Light Microscopy Facility users receive formal and informal training from Nikon engineers, frequent on-site technical support, access to new hardware and software technology, and assistance with cutting-edge experimental set ups.

  • A1R-SIMe: Nikon A1 Resonant Scanning Confocal with Structured Illumination Super-Resolution

    This microscope is very versatile and can be used for live or fixed samples. The resonant scanner allows for very fast acquisitions and the GaAsP detectors are extremely sensitive. The SIM side of the microscope is extremely easy to use with no special sample preparation required for super-resolution imaging.

    • Objectives: 10x, 20x, 40x, 60x, 100x, 60x dry
    • Laser lines: 405, 488, 561, 640nm for confocal; 488, 561, 640nm for SIM
    • Detectors: 5 detectors: 1 transmitted light, 2 high-sensitivity PMTs, and 2 GaAsP detectors; sCMOS for SIM

  • SD: Nikon with Yokogawa Spinning Disk Confocal and Orthogonal Stimulation

    This microscope is great for live cells as it is a low-light technique. With four laser lines and an additional mini-scanner for PA/FRAP/etc., we can easily image dynamic movements in live cells, stimulating/bleaching in real time.

    • Objectives: 20x, 40x water immersion, 40x oil immersion, 60x, 100x
    • Laser lines: 405, 488, 561, 640nm for imaging and 405, 488, 561, 640nm for photoactivation/bleaching/etc.
    • Detectors: Andor EMCCD camera
    • Stage: Piezo

  • LCMD: Nikon with Arcturus Laser Capture Micro-Dissection

    This microscope is really a cellular robot. You can find cells or regions using brightfield or fluorescence that you are interested on tissue slices and draw a line around them, cut them out, move them to a cap and then process the cap for downstream experiments (sequencing, proteomics, etc.).

    • Objectives: 4x, 10x, 40x
    • Laser lines: UV, IR
    • Detectors: Color camera

  • A1R: Nikon A1 Resonant Scanning Confocal with TIRF Module

    This microscope is highly versatile and can be used for live or fixed samples. The resonant scanner allows for very fast acquisitions and the GaAsP detectors are extremely sensitive. This microscope has 6 lasers and the full gamut of objectives and software modules.

    • Objectives: 10x, 20x, 40x, 60x, 100x, 60x TIRF, 100x TIRF
    • Laser lines: 405, 435, 488, 514, 561, 640nm
    • Detectors: 5 detectors: 1 transmitted light, 2 high-sensitivity PMTs, and 2 GaAsP detectors
    • Camera: Andor Xyla

  • A1SP: Nikon A1 Spectral Detector Confocal with FLIM Module

    This microscope is great for fixed samples and is especially useful when experimenters may have overlapping emissions from fluorophores or autofluorescence. The 32-channel spectral detector can be implemented with the click of a button and allows for 32 x 2.5 – 10nm bins of fluorescence identification.

    • Objectives: 10x, 20x, 40x, 60x, 100x
    • Laser lines: 405, 488, 561, 640nm
    • Detectors: 5 detectors: 1 transmitted light, two high-sensitivity PMTs, and 2 GaAsP detectors

  • A1MP: Nikon A1 Resonant Scanning Multi-Photon Confocal

    This microscope is an upright, manual microscope that is suited for in vivo, intravital imaging as well as imaging in and through thick tissues and samples. It uses a tunable infrared pulsed laser to excite fluorophores at the focal volume and features a resonance scanner that can image very quickly along with a fast moving piezo nosepiece. We also have visible lasers for standard upright confocal microscopy.

    • Objectives: 25x extremely long working distance (upright)
    • Laser lines: 760-1040nm
    • Detectors: 1 high-sensitivity PMT, 3 GaAsP detectors

  • HCA: Nikon with High Content Analysis

    This microscope is truly amazing for its ability to collect and automatically
    analyze data from live or fixed samples. The intuitive and adaptive software can be programed to count cells, monitor growth, take high-resolution pictures when a certain feature is found, scan slides, scan multi-well plates, etc. A robot can even load your multi-well plates. It has two imaging paths; wide-field and spinning disk. When it is done, you can have the microscope send you a text message that contains any key variables that you need to know right away.

    • Objectives: All “air” objectives; 10x, 20x, 20xELWD, 40x, 40xELWD, 60x
    • Excitation colors: 395, 415, 445, 488, 515, 540, 590, 640
    • Detectors: Widefield with an Andor Zyla sCMOS camera and also a Crest spinning disk confocal with a ProEM camera.

  • N-STORM: Nikon STORM

    This microscope makes doing 3D STORM imaging straightforward. This has STORM-4.0 which includes a cylindrical lens to provide z-information on your molecules of interest. This also has the option to change not only the TIRF angle with the click of a button, but also the direction of the laser entering the back aperture of the objective.

    • Objectives: 20x, 60x TIRF, 100 TIRF (HP)
    • Laser lines: 405, 488, 561, 640nm
    • Detectors: Hamamatsu ORCA-Flash4.0


  • 3 PC workstations (WS0, WS1, and WS2) with NIS-Elements and other analysis/computational software available.


  Campus Users External Users
Tier 1 Instruments
  • Nikon A1R-MP (Multiphoton)
  • Nikon HCA (High content)
  • Nikon N-STORM (Super resolution)
  • Nikon diSPIM (Selective Plane Illumination)
  • Nikon Micro-dissection
  • FLIM unit from PicoQuant
$28/hour $48/hour
Tier 2 Instruments
  • Nikon Spinning Disk Confocal
  • Nikon A1R Confocal (Scanning confocal)
  • Nikon A1-SP (Spectral confocal)
$18/hour $31/hour
Training $75/hour $130/hour
Rates are subject to change, contact facility to verify current fees.
Updated March 13, 2017

Training for new users consists of:

  • lab safety training,
  • operation of the instrument and associated software,
  • use of data analysis software,
  • exporting or presenting data,
  • clean up and shutdown of the instrumentation.

Once the training is complete, researchers may schedule their experiments through the director of Light Microscopy (James Chambers) or online through FOM (Facilities Online Manager) at

Training generally consists of 2-4 hours per new user and depends on the users previous microscopy experience.  All are welcome, even if you have never used a microscope!

Training #1 can be accomplished with 1-4 people and consists of a demonstration of the microscope hardware and software, discussions of light paths, digital image acquisition, saturation, and features of the microscope.

Training #2 is one-on-one and usually is a brief refresher of training #1 followed by the new user on the microscope acquiring images of a facility-provided sample.  Advanced users can bring their own samples.

Training #3+ is one-on-one and is the time for the user to use the microscope for their samples.  The Trainer will be there to make suggestions/corrections and to be sure the Trainee is going to be able to acquire the data that she/he needs for the project.

Because all of our imaging microscopes run the same software, NIS-Elements, the training for one microscope is transferable to all of the other microscopes.

Advanced Training

The Light Microscope Facility offers free advanced training sessions.  Be sure to be on the Facility Online Manager list to be alerted to these free offering as well as free “pilot data days.”

Facility Online Manager (FOM) (access and reservations)

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User Agreement

  1. When you have questions about anything, ask the director James Chambers.
  2. Treat all equipment with respect.
  3. Do not rush when using the equipment as this leads to breakage/damage that you and your PI will be responsible for replacing.
  4. Use your allotted time and finish on time when someone is on after you.
  5. If you know you will not use your reservation, cancel it ASAP.
  6. Acknowledge use of UMass IALS LMF in all publications. Please use some variant of: “The microscopy data was gathered in the Light Microscopy Facility and Nikon Center of Excellence at the Institute for Applied Life Sciences, UMass Amherst with support from the Massachusetts Life Sciences Center.”
  7. Adhere to the EH&S-approved live cell standard operating procedure when using live samples.
  8. No liquids on the microscope air table.
  9. You are responsible for your data – this means that you should arrange for moving it and backing it up. We will do our best to back it up and preserve it, but it is ultimately the user’s responsibility.