Supported by an expert team, the Notre Dame Integrated Imaging Facility (NDIIF) houses over twenty instruments with comprehensive capabilities to help answer many of the most relevant materials and biological questions researchers have today. Descriptions of each instrument along with their capabilities and rates can be viewed below. 

For more information on using NDIIF instruments and services, including consultations and training, please visit the Use Our Services page 

Electron Microscopy Core

The Electron Microscopy Core integrates a unique bundle of state-of-the-art FEI tools that enable users to attack the most complex modern research problems from micron to Angstrom spatial resolution.

  • Mc 7

    Magellan 400

    A field emission scanning electron microscope (FESEM) with extra high spatial resolution (XHR) which allows sample imaging at extremely low beam energies (<100 eV), avoiding charge effect at non-conductive nano-scale surfaces

  • Mc 7

    Helios G4 Ux Dual Beam

    Designed for the highest-quality imaging, ultra-thin TEM and APT sample preparation, milling and deposition of complex structures with critical dimensions of less than 10 nm, multi-modal subsurface and 3D data collection

  • Mc 7

    Spectra 300

    Spectra 30-300 (S)TEM – the highest resolution, aberration-corrected, scanning transmission electron microscope for all materials science applications

  • Mc 7

    JEOL 2011

    Transmission Electron Microscopy (TEM) 80-200kV, 0.14m, resolution, a workhorse for materials and biological samples 

  • Mc 7

    Leica Automatic Plunge Freezer EM GP2

    For the preparation of vitrified fluid samples for cryo-TEM, including biological suspensions in both, aqueous and inorganic solvents

  • Mc 7

    Leica EM UC7 Ultramicrotome

    The Leica EM UC7 ultramicrotome equipped with the FC7 cryo chamber attachment is capable of preparation of high quality semi- and ultra-thin sections of biological and industrial samples

Optical Microscopy Core

The Optical Microscopy Core provides researchers with the opportunity to acquire informative single images and three-dimensional reconstructions of fluorescently labeled cells and tissues, either fixed or live.

  • Mc 6

    Nikon AZ 100 Marco/Zoom Scope

    The Nikon AZ100 is a multi-zoom macroscope with a wide range of magnification settings (5x-400x) used for either brightfield (top lit or backlit) or contrast imaging

  • Mc 6

    Nikon Eclipse 90i Widefield Fluorescent Microscope

    The 90i is useful for imaging fluorescent or chromogenic (chemically stained) samples such as H&E, immunohistochemistry (i.e. DAB, HRP), Gram, trichrome, and more

  • Mc 6

    GE Healthcare DeltaVision Deconvolution Microscope

    The DeltaVision provides excellent image quality and reduced phototoxicity to allow for long-term, time-lapse imaging in three dimensions - perfect for live cell imaging

  • Mc 6

    Nikon C2+ Laser Scanning Confocal Microscope

    The Nikon C2 confocal system is a semi-automated, upright microscope ideal for imaging fixed samples providing basic confocal imaging with 3 standard PMT detectors and 4 laser lines for four channel imaging

  • Mc 6

    Nikon A1R

    The Nikon A1R inverted confocal system is equipped with four laser lines, 405, 488, 561 and 633nm and a contrast imaging capability and offers high-resolution imaging capabilities for a wide range of imaging applications

  • Mc 6

    Nikon A1R-MP Laser Scanning Confocal Microscope

    The two-photon imaging mode of the Nikon A1R-MP system provides deeper imaging into thick samples with no background resulting from out-of-focus light and minimal phototoxicity in live samples

  • Mc 6

    Bruker Luxendo MuVi SPIM Light Sheet

    The lightsheet system is ideal for long-term, three-dimensional fluorescence imaging of organisms, tissue explants, and 3D cell culture systems. This microscope can be used for live, fixed, and optically cleared samples

  • Mc 8

    Nikon CSU-X1 Spinning Disk System

    The Nikon CSU-X1 is optimized for high speed imaging of living cells expressing fluorescent proteins and/or stained with synthetic fluorescent dyes

  • Mc 6

    Software Analysis - IMARIS

    IMARIS software can be used for image presentation and/or data analysis from a variety of commercial fluorescence microscopy image file formats

In Vivo Imaging Core

The Vivo Imaging Core provides a non-invasive approach to observe various disease and biological conditions in living systems.

  • Mc 6


    A small animal PET/SPECT/CT imaging system

  • Mc 6

    IVIS Lumina

    A benchtop system for 2D bioluminscence, standard fluorescence, and Cerenkov imaging.

  • Mc 6


    An easy-to-use 1 Tesla desktop MRI scanner for small rodents like rats and mice.

  • Mc 6

    MARS Medipix Spectral X-ray CT

    MARS is capable of 3D spectral (multi-energy) scanning coupled with in vivo images for anatomic and molecular quantification

  • Mc 6

    Advanced Molecular Imaging HT Instrument

    Small animal imaging platform capable of capturing luminescent and fluorescent images via a large aperture lens with automation for filter and field of view selection

  • Mc 6


    Body Composition Analysis device for live animals, measuring fat, lean, water and bone mineral content

  • Mc 6

    Scanco VivaCT 80 Micro X-ray CT

    In-vivo microCT scanner offering the largest field of view (80mm) and the best resolution (5µm)

Histology Core

The Histology Core provides a means to examine biological processes in mice, rats, frogs, zebra fish, fruit flies, sheep bone, and even human tissue by use of immunohistochemical techniques and pathology.