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Microscopy & Image Analysis

(formerly the Optical Microscopy and Multiphoton Microscopy, Cell Screening, Electron Microscopy and Histology, X-ray Development and Phosphorimaging Cores) 

For the most updated infomation please visit: 


The WCM CLC Imaging Core Facility provides state-of-the-art instruments and services, and expertise in their applications, to the Weill Cornell Medicine (WCM) community and to outside investigators.  Resources and services include confocal microscopy, wide field fluorescence microscopy, multiphoton microscopy, automated optical microscopy, electron microscopy, histology services (paraffin and cryo sample preparation), phosphorimaging, and X-ray film processing.  The facility provides consultation on project design and image visualization and analysis, and offers seminars, training and educational workshops.



History:  The WCM CLC Microscopy and Imaging Core Facility is the result of consolidation of five previously separate core facilities: Optical Microscopy, Multiphoton Microscopy, Electron Microscopy and Histology, Cell Screening, and X-ray Processing and Phosphorimaging Cores.  These resources are now offered as coordinated services by an integrated core facility. 

Location:  The core is located on the 1st and 2nd floor of the “A” building and X ray and phosophorimaging is in the basement of the "A" building at 1300 York Avenue, New York, NY. There is also a location on the 9th floor of the Belfer Research Building, 413 East 69th Street, New York, NY. 

WCM Core Laboratories Center (CLC):  The WCM CLC was established in 2015.  The CLC includes core facilities that offer resources and services in genomics and epigenomics, proteomics and metabolomics, flow cytometry, imaging (e.g., optical and electron microscopy, high content screening, MRI, PET/CT, and ultrasound), synthetic and analytical chemistry, and nuclear magnetic resonance (NMR).

Open to all:  The resources and services of the core facility are open to all investigators at Weill Cornell Medicine, Cornell University and Cornell-affiliated institutions.  The facility also provides services to external investigators at both academic institutions and commercial enterprises.


Confocal microscopy

Confocal Microscopy: Zeiss LSM 880, Zeiss LSM 880 + AiryScan, and LeicaSP5.  Features include: multiple wavelength imaging of thick samples; imaging of fixed and live cells, tissue, and 3D cultures; super-resolution (32-element Airyscan detector); spectral imaging (32-channel GaAsP array); “filterless” acquisition (custom emission bandwidths); tile scanning; complex time lapse experiments.  Laser excitations: 405, 458, 488, 514, 561, 594, 633 nm.  Objectives: 10x, 25x, 40x, 63x, 100x (all but 10x are oil immersion; all DIC for simultaneous transmitted light imaging). For more information on this service visit: Confocal Microscopy 

Widefield fluorescence microscopy

Wide Field Fluorescence Microscopy:  Zeiss AxioObserver (inverted) and Zeiss AxioPlan (upright).  Features include: multiple wavelength fluorescence and transmitted light imaging; imaging of cell cultures and tissue sections; tile scanning; basic filter cubes (blue, cyan, green, red, far red); 5x – 63x objectives; CCD camera. For more information on this service visit: Widefield Microscopy

Multiphoton Microscopy

Multiphoton Microscopy: Olympus FluoView FV1000MPE with Mai Tai DeepSee laser.  Features include: fluorescence, autofluorescence and second harmonic imaging of cells, 3D cultures and thick tissues; intravital imaging (mice/rats); inhalation anesthesia equipment; oxygen supply; heated stage and circulating-water heating blankets; excitation laser tunable between 690 - 1040 nm; simultaneous detection of up to 4 signals; additional 405 nm laser (for uncaging and photoactivation).  Objectives include standard ones, plus low-power large field-of-view macro lenses: 2x and 4x.  IR-transmitting, high NA water-immersion objectives: 10x/0.6NA and 25x/1.05NA.  Small tip diameter microprobe objectives: 6x and 20x; tip diameter: 1.3 mm; water-immersion. For more information on this service visit: Multiphoton Microscopy

Automated Optical Microscopy

Automated Optical Microscopy:  ImageXpress Micro Imager.  Features include: automated fluorescence imaging of fixed- or live-cells; inverted wide-field fluorescence microscope designed for rapidly imaging cells in multi-well plates; compatible with 6, 24, 96, 384 and 1536-well plates; high-speed laser autofocus allows for imaging of up to 100 plates/day; imaging of up to 5 different wavelengths from UV to near IR; long working-distance objectives from 2X to 60X; unattended screening of up to 45 plates/run; MetaXpress software and MDCStore integrated database with >5TB of ITS supported server space for images.  Automated sample prep facilitated by two MultiDrop384 Dispensers and a BioTek Plate Washer. For more information on this service visit: Automated Optical Microscopy

Electron microscopy

Electron Microscopy:  JEOL JEM 1400 Transmission Electron Microscope (TEM).  Features include: accelerating voltage up to 120 Kv and two digital CCD cameras for rapid (2K x 2K) or high-resolution (11 Megapixel) imaging.  Two ultramicrotomes for sectioning EM samples; vacuum evaporator for carbon coating; glow discharger; critical point dryer and sputter coater for SEM sample prep. For more information on this service visit: Electron Microscopy

X-ray film processing

X-ray film processing: Two Konica SRX-101 X-ray film processors. 


Phosphorimaging: GE Typhoon Trio PhosphorImager.  Applications include acquiring images of 1D or 2D gels, blots, tissue sections, etc. using either storage phosphor screens, chemiluminescence or specific fluorescent stains excited by red (633 nm), green (532 nm) or blue (488 or 457 nm) light. Protein or nucleic acid determination can also be done in microtiter plates when stained with appropriate fluorescent dyes.  Data can be quantitated using available ImageQuant software.

Image visualization and analysis

Image Visualization and Image Analysis:  Available software: MetaMorph, ImageJ/Fiji, Zeiss Zen,  Imaris Autoquant Image Deconvolution; MetaXpress. For more information on this visit: Image analysis

Histology Services

Histology Services:  Tissue embedding, sectioning, and staining.  Features include: Hacker-Bright OTC cryostat; two Leica RM2155 rotary microtomes; two TissueTek VIP150 paraffin tissue processors.

Seminars, workshops and training


Optical microscopy: Three confocal microscopes (Zeiss LSM 880; Zeiss LSM 880 + Airy Scan with 32-channel GaSP array for spectral imaging and incubation chamber for long-term live cell imaging; Leica SP5), multiphoton microscope (Olympus FluoView FV1000MPE, with auxiliary mouse pulse oximeter, anesthesia and euthanasia equipment), Zeiss AxioObserver inverted microscope, Zeiss AxioPlan upright microscope, dissection stereomicroscope (Olympus SZX16). 

High content screening: ImageXpress MICRO High Content Analysis Imager, Thermo CataLyst Express Robotic Plate Loader, two MultiDrop384 Dispensers, BioTek ELx405 Microplate Washer. 

Electron microscopy: Electron microscope (JEOL JEM 1400 TEM with 2 cooled Olympus-SIS CCD cameras, 2K x 2K Veleta and 11 Megapixel Quemesa), two ultramicrotomes (Leica Ultracut S, Leica UltraCutT), Electron Microscopy Science Vacuum Evaporator, Pella EasiGlow glow discharge unit, Electron Microscopy Sciences Critical Point Dryer, Pelco 91000 Sputtering Unit. 

Histology: Two TissueTek VIP paraffin tissue processors & embedding station, two Leica RM2155 rotary microtomes, Hacker-Bright OTC cryostat. 

X-ray film developing:  Two Konica SRX-101 X-ray film processors. 

Phosphorimaging: GE Triad Typhoon laser scanner. 

Image analysis: 4 image analysis workstations.

Contact Information

Lee Cohen-Gould, M.S., CEMT
Director of Optical Microscopy, Electron Microscopy & Histology Services
WCM CLC Imaging Core Facility
(212) 746-6146


Sushmita Mukherjee, Ph.D.
Director, Optical Microscopy and Image Analysis Services
WCM CLC Imaging Core Facility
(212) 746-6495


H. Skip Ralph, MPA
Director of Automated Optical Microscopy
WCM CLC Imaging Core Facility
(212) 746-6480

More Information

For more information about services and pricing, to register as a user of the core, to submit samples, to schedule time on the instruments, and/or to arrange for training, please go to the WCM iLab portal at

For more information about services and the core please visit:

Contact Information

Core Contact: Lee Cohen-Gould, M.S.


Phone: (212) 746-6146