Central Microscopy Imaging Center (CMIC)




Overview of Services


CMIC at Stony Brook University is a comprehensive core service center maintained and managed by the Office of Scientific Affairs (OSA) in the Renaissance School of Medicine. It provides a wide spectrum of multiscale microscopy services including confocal microscopy, two-photon microscopy, super-resolution microscopy, transmission electron microscopy (TEM), focused ion beam-scanning electron microscopy (FIB-SEM), atomic force microscopy (AFM), electron microscopy sample preparation, and thermomechanical analysis services. CMIC with the state of the art microscopy instrumentation serves the internal and external clients in medicine, life sciences, engineering, physics, and chemistry communities. The singular goal of the CMIC is to facilitate and support the research enterprise not only at Stony Brook University but also around the Long Island area and beyond.

CMIC operates as two facilities separately:  1. Optical Microscopy facility, 2. Electron Microscopy (EM) facility.

CMIC has two locations: (1) west main campus, (2) Research & Development Park.


  1. Optical Microscopy Facility Instrumentation

         (1) Zeiss LSM 980 with Airyscan 2 NLO Two-Photon Laser Scanning Confocal Microscope System (Life Sciences building, west main campus)

  • Inverted Axio Observer 7 with definite focus.3 motorized condenser for AI based automated sample finder and motorized XY stage.
  • Airyscan 2 multiplex high speed, 32-channel GaAsP detector, joint deconvolution, super-resolution (90nm).
  • 2 MA-PMT+1 GaAsP detectors for regular confocal or 2P lasers, 1 transmitted light T-PMT for widefield imaging.
  • Laser lines: 405nm, 445nm, 488nm, 561nm, 639nm, MaiTai HP tunable 2P laser: 680nm – 1040nm.
  • Objectives: 10X, 20X, 40X, 63X, 100X.
  • Equipped with a dark heated incubator chamber for live imaging.
  • Equipped with a LSM Inverter for upright application with 2P system.
  • Capable of FRAP, FLIP, FRET, 3D, spectral unmixing, colocalization, ROI measurement, line and spot scan, multiposition assay, time lapse, photo-activation, live cell imaging, and small live animal imaging.    

     (2) Nikon N-SIM Super Resolution Microscope System (Life Sciences building, west main campus)

  • N-SIM (Structured Illumination Microscopy): resolution 100nm, 2x higher resolution than conventional microscopy.
  • Inverted Nikon Eclipse Ti research microscope with a motorized stage.
  • 100x objective only for N-SIM imaging.
  • Laser lines: 405nm, 488nm, 561nm, 640nm.
  • 3D capable

     (3) Nikon N-STORM Super Resolution Microscope System (Life Sciences building, west main campus)

  • N-STORM (Stochastic Optical Reconstruction Microscopy): resolution 20nm, 10x higher resolution than conventional microscopy.
  • Inverted Nikon Eclipse Ti research microscope with a motorized stage.
  • Laser lines: 405nm, 488nm, 561nm, 647nm.
  • 3D capable, TIRF capable. 

          STORM Protocol-Sample Preparation

    (4) Leica TCS SP8X Laser Scanning Confocal Microscope System (AERTC building, R & D Park)

  • Upright Leica DM 6000 microscope with a motorized XY-Stage.
  • Laser lines: White Light Laser (WLL) 470-670 nm), UV 405 nm. Detection range: 400-800 nm.
  • Internal detection channels: 2xPMT, 2x HyD.
  • Equipped with Tokai Hit Stage Incubator providing 37˚ C and 5% CO2 for live cell imaging.
  • Tandem scanner 8 KHz with non-resonant mode and resonant mode.

    (5) Zeiss LSM 510 META Laser Scanning Confocal Microscope System (Life Sciences building, west main campus)

  • Inverted Zeiss Axiovert 200M microscope with a manual control stage.
  • Laser lines: 458nm, 477nm, 488nm, 514nm, 543nm, 633nm.
  • Equipped with incubator chamber and a Zeiss CTI-Controller 3700 for CO2 and temperature control for live cell imaging.
  • Capable of FRAP, FLIP, FRET, 3D, time lapse, photo-activation, and spectral imaging.

     (6) Two Workstations (Life Sciences building, west main campus)

  • One standalone workstation with Nikon NIS-Element (Ar) software, STORM images, and SIM images off-line analysis licenses.
  • One standalone workstation with Zeiss LSM software (version 4.0) off-line image analysis license.

     (7) Preparative Equipment (Life Sciences building, west main campus)

  • Cell culture room equipped with Class II Biological Safe Cabinet (Baker Company), CO2 Incubator (SANYO), 4 Co Refrigerator.


2. Electron Microscopy Facility Instrumentation

      (1) FEI BioTwinG2 Transmission Electron Microscope (TEM) (Life Sciences building, west main campus)

  • Acceleration voltage of 120kV.
  • Goniometer/stage tilt capability.
  • AMT XR-60 CCD digital camera system for acquiring digital images.
  • Film capability.

    (2) JEOL JEM 1400 Transmission Electron Microscope (TEM) (AERTC building, R & D Park)

  • Illumination Emitter: Precentered single-crystal La B6 filament
  • Resolution: 0.2nm/0.38nm(Lattice Image/Point Image)
  • Accelerating Voltage(Steps/Varaible steps/Stability): 40, 60, 80, 100,120kV /33Vmin. step/2x10-6 per min
  • Magnification(Mag mode/Low Mag mode): x5K-2M/x120-4K
  • Equipped with anti-contamination device and cryofin
  • Equipped with Gatan Orius SC1000B CCD camera
  • Equipped with energy dispersive X-ray and Oxford X-MAX 80T detector

   (3) Zeiss Crossbeam 340 focused Ion Beam-Scanning Electron Microscope (FIB-SEM) (AERTC building, R & D Park)

  • FE-SEM, High Vacuum or Variable pressure mode available
  • Multiple detectors available: InLens Duo(SE and BSE), SE2, VPSE
  • Capella FIB column with Ga-Liquid metal ion source
    • Resolution at 30kV:3nm
    • Voltage range:500V-30kV
    • Probe Current range: 1pA-100nA        
  • Equipped with Micromanipulator, capable of TEM lamellas specimen preparation
  • Equipped Gas Injection System of Platinum precursor
  • Equipped with Oxford EDAX and EBSD detectors
  • Equipped with Leica cryo system
  • Equipped with Atlas5, a powerful integrated software, capable of 3D tomography imaging and nano-patterning process

    (4) Sample Preparation ((Life Sciences building, west main campus, and AERTC building, R & D Park)

  • Leica EM UC7 Ultramicrotome
  • Leica EM UC7/FC7 Ultramicrotome and Cryo-ultramicrotome
  • Freeze Plunger FEI Vitrobot
  • High Vacuum Coater/Freeze Fracture Unit Leica EM ACE 600:
    • Euipped with cryo-transfer SEM sample holder(Leika VCT 100) for Cryo-SEM sample prep
  • Turbo Freeze Drier EMS 775
  • Cryo Transfer TEM Speimen Holder(Gatan Gat-626)


3. Bruker Dimension ICON Atomic Force Microscope (AFM) (AERTC building, R & D Park)

  • Multimode available.
  • Heating and Cooling from -35˚C to 250˚C.
  • Scanner specifications: 90 µm X 90 µm in X-Y direction; 6 µm in Z direction.
  • Sample size ≤ 200 mm (8 inch) in diameter and ≤ 15 mm (0.65 inch) in thickness.
  • Applications: materials mapping, nanomechanics characterization, nanoelectrical characterization, biological characterization


4.Thermomechanical Characterization Instrumentation (AERTC building, R & D Park)

      (1) Dynamic Mechanical Analysis (DMA) - TA Q800

  • Temperature range: -145∼600°C
  • Force range: 0.0001∼18N
  • Frequency range: 0.01∼200Hz
  • Available clamps: Dual/ Single cantilever, compression, 3-point bending, tension (Film)

     (2) Thermal Gravimetric Analysis (TGA) - TA Q50

  • Monitoring weight changes in a materials as a function of temperature and time
  • Temperature range: ambient+5∼1000°C
  • Sensitivity: 0.1μg

     (3) Differential Scanning Calorimetry (DSC) - TA Q2000

  • Measure temperature and heat flow associated with thermal transitions in a material
  • Temperature range: -90∼550ºC
  • Tzero Hermetic pans available for liquid and volatile samples

     (4) Thermal Conductivity Meter - DTC-300

  • Measure thermal conductivity of a material accordance with the ASTM E1530 standard
  • Temperature range: -20∼300°C
  • Thermal conductivity range: 0.1∼40W/m.K
  • Specimen size: 2" in diameter, ≤1" in thickness




Glen Itzkowitz, Associate Dean, Office of Scientific Affairs (OSA), Renaissance School of Medicine

Jorge L. Benach, PhD, Distinguished Professor, Vice Dean for Research, Renaissance School of Medicine


Location and hours of operation




9:00am to 5:00pm      

Monday through Friday

  • Main West Campus:

        100 Nicolls Road

        048 Life Science Building
        Stony Brook University
        Stony Brook, New York 11794-5200

  • Research & Development Park:

       1000 Innovation Road

       113 Suit, AERTC Building
       Stony Brook University
       Stony Brook, New York 11794-6044

Links and Resources


  1. CMIC Website
  2. Office of Scientific Affairs (OSA)
  3. FEI
  4. Nikon
  5. N Storm Sample Submission Protocol
  6. Leica Microsystems
  7. Zeiss
  8. ImageJ


Links to Software Tutorials

New Users: Logging In and Getting Started in iLab

Managing Lab Settings (for Lab Managers and PIs)

Making Service Requests

Making Equipment Reservations


Name Role Phone Email Location
Guowei Tian (Light Microscopy)
Light Microscopy Facility Manager 
(631) 632-9331
048 Life Sciences Building
Yunming Hu (EM)
EM Facility Manager 
(631) 632-8623 
046 Lif Sciences Building