Microscopy Imaging Facility

The Microscopy Imaging Facility at Penn State College of Medicine provides services and consultation in ultra-high-resolution imaging of cells and tissues in fixed or live states. We also provide expert services in quantitative image analysis and consultations on microscopy-related research projects.

Our Confocal and Deconvolution Microscopes are useful in 3D imaging of any biological systems and spatial distribution of multiple fluorescently-labeled sub-cellular objects, including various cellular proteins complexes (multiple colors) simultaneously in live or fixed biological conditions.

We are also equipped with a Multimodal Multiphoton Microscope, which is capable of performing deep tissue fluorescence (multiple colors) and harmonic generation imaging in ex vivo, in vivo or intra-vital small animal imaging.

Our IMARIS, VOLOCITY and HUYGENS Workstations are excellent tools for 3D reconstruction from a series of 2D optical sections as well as complex quantitative microscopy computations.

Our Cryo- and Transmission Electron Microscopes enable ultra-high-resolution 3D imaging of sub-cellular objects as small as protein complexes and antigen-antibody interactions at the ultra-structural level.

Our Auto3dem and EMAN2 Workstations are useful for cryo-TEM image processing and  3D reconstruction.

View the full Microscopy Imaging Facility brochure here (PDF).

Scheduling Calendar

To reserve time on one of our Light Microscopes or TEM, please use our calendar here.

All potential users of Light Microscopes are required to have completed training prior to using the microscopes. Please contact Dr. Thomas Abraham at tabraham1@hmc.psu.edu to arrange training or consultations.

Please review the following documents before accessing the scheduling calendar:


Leica SP8 Inverted confocal (Room C1730) is  capable of generating submicron level spatially and spectrally resolvable multicolor 3D or 4D fluorescent images in live or fixed cells/ tissues.

  • Tunable emission filter technology (AOBS) and tunable pulsed white light laser source
  • Fully automated operational procedures
  • High numerical aperture immersion objectives
  • Differential interference contrast (DIC) imaging
  • Line and area scanning capabilities with simultaneous or sequential scanning options
  • Ultra-high-speed live cell imaging, complex cell tracking experiments, FRAP measurements, ratio metric experiments, complex FRET measurements,
  • Tile scanning (scanning whole slide)
  • Hybrid signal detection systems which allow 3D or 4D image generation at much lower light energies
  • Time-gated fluorescence signal collection and single photon counting
  • Sophisticated live cell stage heater and CO2 chamber for perfusion system (Tokai Hit, Japan) that enables complex live cell experiments continuously for several days

Fluorescence Microscope

DeltaVision Elite Inverted Microscope (Room 1728) is uniquely designed for generating multicolor 3D or 4D fluorescent images in ultra-high speed live cell imaging mode as well as ultra-fast  tile scanning mode.

  • Precise optical sectioning capability and deconvolution software
  • Multi-wavelength switching excitation light source
  • High numerical aperture immersion objectives
  • Highly sensitive cooled CCD and EM-CCD cameras
  • Differential interference contrast (DIC) imaging
  • Tile scanning (scanning whole slide)

Multiphoton Microscope

Nikon A1 MP+ with Spectra Physics Insight DeepSee Femtosecond Laser (Room 1730) is designed for high-resolution ultra-high speed deep tissue ex vivo, in vivo or intra-vital small animal fluorescence (multiple colors) and harmonic generation imaging in upright microscope platform.

  • Ultrahigh-speed hybrid scanning capabilities
  • Ultrashort pulse IR laser tunable from 680-1300 nm
  • Highly sensitive GaAsP detection systems
  • Low magnification high resolution water dipping objective lens
  • Tile scanning (scanning whole slide)
  • Fast video rate imaging enabling deep tissue visualization of rapid reactions in living organisms, including dynamics and cell interactions  and various other physiological events in real time

Transmission Election Microscope

Our JEOL 1400 TEM (Room C1727) is capable of generating ultra-structural nanoscale images from fixed cell/tissue samples or multiplexed immune-labeled samples.

  • Computer-controlled operations
  • Resolution up to 3 Angstroms
  • Magnification up to 370,000X
  • Capable of collecting data suitable for 3D reconstructions of negative-stained samples

Cryo-Electron Microscope

Our JEOL 2100 Cryo-EM (Room C1724) collects data that can be processed into high resolution 3-D maps. Samples in solution are vitrified, preserving biologically relevant structures samples include:

  • Small proteins
  • Large whole cells and sub-cellular environments
  • Dynamic complexes

The JEOL 2100’s tilt stage and SerialEM software also enable 3D tomography.

3D and 4D Fluorescence Image Processing Stations

Our IMARIS, VOLOCITY and HUYGENS (Room C1732A) image processing work stations facilitate 3D and 4D reconstructions to visualize and analyze multiple color images from fluorescence and confocal microscopes.

  • Surface renderings
  • Deconvolution
  • Segmentation
  • Fluorescence intensity measurements
  • Complex cell tracking measurements
  • Voxel counting
  • Batch processing
  • Drug bio-distribution measurements
  • Accurate colocalization analysis
  • Many other complex image processing, statistical calculations depending upon researcher’s needs

Cryo-EM Image Processing

Auto3dem or EMAN2 (Room C1725) work stations enable 3D reconstruction and visualization of Cryo-EM images.

PyMOL, Chimera, Veda, or Situs software program facilitates fitting, and interpretations of Cryo-EM data.

Fee Schedule

Please email Kathy Stauffer at kstauffer2@hmc.psu.edu for updated user fee info.

Microscopy Imaging Facility sample photos


Microscopy Imaging Facility examples


For photos of Cryo-EM work, see the gallery here..

Contact Us

Scientific Director

Thomas Abraham, Ph.D.
(717) 531-0003, ext. 285486
See details in Penn State Profiles

Cryo-EM Lab

Susan Hafenstein, Ph.D.
Cryo-EM Director
(717) 531-0003, ext. 281269
See details in Penn State Profiles

Bob Ashley, AAS
(717) 531-0003, ext. 289256

Confocal Lab

Wade Edris, MS
(717) 531-1157


Han Chen, MD, Ph.D.
(717) 531-4036