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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.


  • Tokai Hit on-stage incubator with CO2 , heat, and humidity
  • Oko Lab on-stage incubator with CO2 , heat, and humidity
  • 4 full size incubators available for use (one has O2 control) Experiments are performed in solution and precious samples may be retrieved.
  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

Facility Online Manager (FOM) (access and reservations)

James Chambers, PhD

Developing photochemical molecules and techniques as well as new imaging modalities since 2002. His deep yet varied experience allows him to convey expertise in acquisition recommendations, data optimization, and manual and automated analysis of large numbers of images.

Facility Staff

James ChambersJames Chambers
(413) 577-4580

Patricia WadsworthPatricia Wadsworth
(413) 545-4877


S576A Life Science Laboratories
University of Massachusetts Amherst
240 Thatcher Road
Amherst, MA 01003

  • I have only been using the SIM and STORM microscopes at the UMass light microscopy facility for a few months and already it seems like my data has the potential to transform my thesis project. Thanks to the guidance and help from the facility manager (Jim) I have been collecting images that have changed my approach completely and might lead to some pretty exciting findings in my field. The facility manager has been more than patient while training me, has provided valuable advice and makes the facility a pleasant and productive environment, constantly striving to improve it. I am excited to continue to work and collect data that can impress any audience, and of course push my field forward!

    — Emily Melzer

  • I am a graduate student currently using the N-STORM microscope over at the LMF and Jim has been of great help to me and my project. He trained me to use the microscope and to analyze the data obtained. He also helped me troubleshoot the settings to acquire my data as well as being present in the LMF should any problem come up. He is very welcoming, helpful and if he does not know the answer he makes sure to get backup from the NIKON representatives in order to help me solve any issue.

    — Ana Torres-Ocampo

  • The facility is very useful to our research. It has more than 6 types of confocal microscopes. Depending on research purposes, we can use proper microscopes. Our samples are not typical samples such as cell. However, these variety of microscopes make it possible to adjust conditions to our specific samples.
    Dr. James chambers, who is in charge of the facility, is very helpful, helping students to optimize the experimental conditions as well as to build customized setups for each experiments. We frequently discuss experimental setups with him and he always gives us great ideas on the experiments. He also teaches both basics and advances on confocal microscope, trying to help students to understand the mechanics of the microscope. He is always improving the facility and maintain the facility in an excellent shape. Nikon researchers are also helpful and they give us quick useful feedback when we have some questions and concerns on the microscopes.

    — Tetsu Ouchi

  • The microscopy facility LMF at UMASS Amherst is the kind of facility that I was looking for years. So glad that it finally happened! Just in less than two months, we generated enormous amount of data (!) and helped writing two papers, one already published, and the other under submission. It has so many different kinds of microscopes and I can definitely say from my experience that the center is a place to explore science. And the director of the center, Dr. James Chambers, is always there to help you.

    — Rubul