Within the Microscopy and Advanced Bioimaging CoRE, we use a number of microscopes, including:

• Widefield Microscopes 
  • Zeiss Axio Imager.Z2 (2x) with motorized XYZ movement 
  • Leica DMi8 for live-cell microscopy 
  • Olympus MVX10 macroscope 
  • Zeiss Axioplan 2ie for polarized light microscopy 
  • Olympus IX71 for simple screening 

• Confocal Microscopes
  • Super-resolution: Leica TCS SP8 with STED 3x and White Light Laser 
  • Super-resolution: Zeiss LSM 880 Airyscan with 32-linear spectral GaAsP array + PMTs and the Airyscan detector  
  • Super-resolution: Zeiss LSM 980 Airyscan with 32-linear spectral GaAsP array + PMTs + 2 NIR GaAsP detectors and the Airyscan detector 
  • Leica Stellaris 8 with White Light Laser and 4 spectral Power HyD detectors 
  • Leica TCS SP8 with spectral detector 
  • Zeiss LSM 780 with 34-channel spectral detector 
  • Yokogawa Spinning Disk, built on Zeiss Axio Observer.Z1 

• Multiphoton Microscopes
  • Olympus FVMPE-RS-with Dual Line Insight X3 laser 
  • Olympus FV1000 with Coherent Chameleon Vision II laser

• Lightsheet Microscope
  • LaVision Biotec UltraMicroscope II (zoom and infinity optics available) 

• High-Content Screener 
  • ThermoFisher CX7 LZR 

• Transmission Electron Microscope
  • Hitachi 7500  
  • Hitachi 7700 

The CoRE provides a range of Light Microscopy applications, including:

• Whole organ/organism live/fixed imaging
• Whole organ/organism fluorescence imaging
• Super-resolution confocal imaging
• Spectral unmixing for multiplexed samples
• High-resolution widefield with deconvolution processing available
• Fast, high-resolution live-cell imaging with Yokogawa Spinning Disk
• FLIM, FCS and FRET
• High-content imaging
• Optogenetics and electrophysiology
• Intra-vital imaging

This automated, upright widefield microscope from ZEISS is ideally suited for imaging standard glass slides containing fixed- or live-cell samples. Color and monochrome cameras are available for Brightfield/Phase/DIC and fluorescence imaging, respectively. A ten-position filter turret gives the Imager.Z2(M) large flexibility in the fluorophores it can image, without the need to stop and swap filter sets.

ZEISS' ZEN blue software package controls the microscope and offers multi-color imaging in conjunction with tile scanning, Z-stacking, and time-series acquisition. Advanced tiling functionality allows users to easily incorporate a focus map that accurately follows the changing plane of sectioned tissue. Capturing Z-stacks to account for focal disparities is no longer necessary, and file size on large tile images is greatly reduced.

The ApoTome.2 optical sectioning device offers confocal-like image quality through structured illumination. Compatible with all lenses and filter sets, ApoTome.2 improves fluorescence image quality by filtering out-of-focus light to reveal detail in just the focal planes of interest.

This automated upright widefield microscope from ZEISS is optimal for imaging standard glass slides containing fixed samples. Color and monochrome cameras are available for Brightfield/Phase/DIC and fluorescence imaging, respectively. A 10-position filter turret gives the Imager.Z2 large flexibility in the fluorophores it can image without the need to stop and swap filter sets.

ZEISS' ZEN blue software package controls the microscope and offers multi-color imaging in conjunction with basic tile scanning, Z-stacking, and time-series acquisition.

The ApoTome.2 optical sectioning device offers confocal-like image quality through structured illumination. Compatible with all lenses and filter sets, ApoTome.2 improves fluorescence image quality by filtering out out-of-focus light to reveal detail in just the focal planes of interest.

Resources for the Zeiss AxioImager.Z2 for fixed- or live-cell samples include:

Fluorescence Protocol

Transmitted Light Protocol

This flagship inverted microscope from Leica features a motorized XY stage for tiled fields and Navigator software module for automated tile acquisition; a TokaiHit stage-top incubation system and time-lapse module for long-term live-cell imaging; and a SpectraX four-LED illumination system capable of fast, multi-color widefield fluorescence imaging.

The system is equipped with color and monochrome cameras for Brightfield/Phase/DIC and fluorescence imaging, respectively. Operated via Leica's LAS X software suite, the DMi8 easily images live- and fixed-cell samples in Petri dishes, well plates, chamber slides, and standard glass slides. Fast widefield FRET imaging (CFP/YFP) can also be configured. Injection of drugs is possible via openings in the stage-top incubation system. 

This automated inverted microscope has multiple features to enable long-term time-lapse imaging experiments: a LiveCell enclosed chamber that permits temperature, CO₂, and humidity control; adapters for well plates, dishes and slides; and a Ludl motorized stage and focus motor that can be used to mark multiple sites in xyz. Images are captured with a Q Imaging Retiga 2000R cooled CCD camera; 1600 X 1200 pixels, 7.4µm X 7.4µm per pixel, sensitivity is high and linear through ~550nm and then decreases linearly between 600nm to ~900nm. Exposure to light is controlled by Uniblitz shutters.

The system is controlled by MetaMorph software. Prior to imaging, an on-site tissue culture incubator is available to house cells. Typical uses for this system include cell tracking, neurite growth, cell motility, wound healing, and Fura-2 imaging.

The Axioplan 2ie is optimal for studies of samples under polarized light. Standard glass slides can be examined under linear and circularly polarized light, and basic brightfield is available as well. The AxioCam MRc camera coupled with AxioVision software creates a simple-to-use polarized light imaging system.

This manually controlled Olympus stereoscope is ideal for imaging whole organs or even entire embryos stained with brightfield or fluorescent markers. The system features a dual-chip Olympus DP80 camera, which allows researchers to easily switch between a color sensor for brightfield imaging and a monochrome sensor for higher-sensitivity fluorescence imaging. Larger, tiled fields can be built manually by the user. A 10x zoom factor coupled with optional 0.63x, 1.0x, and 2.0x front lenses permits a large range of magnifications for imaging. The MVX10 is controlled by Olympus' cellSens software suite.

The Leica Stellaris 8 microscope is a confocal imaging system designed to maximize the number of probes and photon collection sensitivity for a range of applications, including fixed and live samples.

The Stellaris 8 is equipped with several technologies that allow it to achieve both versatility and sensitivity. A white light laser can pump eight individually tunable and simultaneous laser lines, and it is tunable from 440 nm to 790 nm in 1nm steps. The system features an additional UV405 Diode Laser, bringing the total simultaneous usable lasers to nine. The system is also equipped with four spectral Power Hybrid Detectors, which have a detection range from 405nm to 850nm, a photon sensitivity of up to 58 percent, and a dynamic range up to 180MCounts/s.

The spectral capabilities of the Stellaris 8 are further enhanced by TauSense technology. TauSense allows real-time separation of fluorophores based on their lifetime properties. It achieves this by computing the distribution of the average arrival time of photons. The user is then able to separate fluorophores or remove auto-fluorescence based on these lifetime properties. Tiling and imaging ROI samples is easily achieved in the navigator interface, and an Okolab incubation box controls temperature, humidity, and CO2. 

The Stellaris 8 system is additionally equipped with lightning super-resolution, a deconvolution-based strategy (Richardson-Lucy algorithm coupled to a statistical decision mask that computes SNR in voxels of data), that can improve resolution to 120 nm in the lateral dimension and 200 nm in the axial dimension. The algorithm can run in a global or adaptive setting, depending on the user selection, while preserving the sum of photons in the volume and raw confocal data and runs in near-real-time on up to five simultaneous detection channels without the need for calibration.

The Zeiss LSM 980 is equipped with Airyscan 2 for super-resolution imaging. The microscope is optimized for simultaneous spectral detection of multiple weak labels, from 405 to 730nm excitation, with high efficiency. The availability of 405, 445, 488, 514, 561, 594, 639 and 730 nm laser lines and an ensemble of two multi-alkaline PMTs, 32-channel spectral GaAsP, and 2 near-IR GaAsP detectors can accommodate a multitude of fluorophore configurations. The software can also automatically perform experiments like FRAP, FCS, spectral unmixing, linear unmixing with fingerprinting, and large area 3D tiling.

Airyscan 2 is an area detector with 32 circularly arranged detection elements, each of which acts as a small pinhole contributing to super-resolution information, allowing for a resolution of up to 120nm. The Airyscan 2 can also operate in two different multiplex modes to combine super-resolution with high acquisition speed by using parallel pixel readouts. The high sensitivity of the detector, combined with the low excitation laser power required and the fast acquisition speeds, makes the Airyscan 2 ideal for sensitive live-cell time series. It can additionally perform ultrafast time series of single slices, tiling of large areas, or volumetric time-lapse imaging.

The system features a full incubation suite for temperature, humidity, O2, and CO2 control, making it optimal for live-cell studies, as well as for inducing hypoxia. The microscope is equipped with a piezo Z-drive, definite focus, and the AI sample finder to automate focus adjustment and identify the relevant imaging regions on the carrier, thus reducing the time to set up the imaging experiment.

The microscope is also equipped with an LED illuminator (Colibri 385, 475, 555, 630nm), a quad cube (DAPI/GFP/Cy3/Cy5), and a widefield camera for fast widefield experiments that can take advantage of the AI finder, incubation, and autofocus hardware.

The Leica TCS SP8 sits on an inverted Leica DMi8 microscope stand and includes five lasers: a UV Diode (405nm), an Argon laser (458nm, 488nm, 514nm), a 561nm, a 594nm and a 633nm. Its spectrophotometer scan head is comprised of one PMT and three HyD detectors, which are more sensitive for weaker signals, to detect five different tunable emission wavelengths, as well as a transmitted light detector for the addition of DIC imaging.

The motorized stage and Navigator software package allow the user to map large sample areas at high resolution in addition to imaging multiple, non-contiguous single positions. Full OkoLab incubation is available for live-cell experiments as well, with hardware controlled by Leica LAS X software. Leica’s “lightning” mode is also available, which offers 40 frames-per-second multi-color imaging at 512x512 pixels, down to 120nm lateral resolution.

Long considered a workhorse of the Microscopy CoRE, the Leica SP5 is a seven-laser line inverted imaging system with many capabilities. The Leica SP5 features six detectors for simultaneous imaging (four PMT, one HyD, T-PMT); a high-speed resonance scanner for up to 25 frames-per-second at 512x512 resolution; a full temperature- and CO₂-controlled incubation chamber; the ability to perform multiple types of FRET imaging; and the ability to perform spectral scanning to accurately separate overlapping emission spectra.

Its motorized XY stage easily adapts to different sizes of dishes, chamber slides, and standard glass slides. The LAS AF software suite makes setup and image acquisition easy, while giving users the opportunity to expand on their imaging capabilities as their needs evolve.

Building on the powerful Leica SP8 confocal scan head, this super-resolution system features three separate additional lasers for stimulated emission depletion (STED) across a range of fluorophores. The STED 3x setup provides XY resolution down to 50 nanometers and improved point spread functions, allowing for optimal resolution with any sample.

In addition to five standard laser lines and five detectors (two PMT, three HyD), the STED system has a pulsed tunable white light laser that will excite fluorophores from 470-670nm. The white light laser gives users the ability to precisely maximize excitation efficiency of one fluorophore at a time in multiplexed samples while also enabling the use of advanced imaging techniques such as FLIM, which requires a pulsed laser. The pulsed white light laser, coupled with the pulsed STED 775nm laser line, even allows for FLIM STED, a super-resolution technique that permits separation of emission signals based on temporal data.

Tau STED, the latest addition to this system, aids researchers with time-correlated photon counting, giving users the unique ability to separate fluorescence signals based on time-of-detection and the actual number of photons collected. Availability of phasor plot analysis tools with the module enables effective FLIM and FRET-FLIM studies.

Harnessing the power of a 32-channel, honeycomb-shaped array detector, the LSM880 with Airyscan offers super-resolution microscopy without the complications of restricted sample preparation or fluorophore choice. This means that if a user’s sample is compatible with a standard confocal microscope, it is compatible with the super-resolution Airyscan detector as well. Resolution improvements up to 140nm in XY and 400nm in Z are possible in combination with imaging speeds of up to 13 frames per second at 512x512 resolution.

The LSM 880 with Airyscan is built on the inverted Axio Observer.Z1 microscope and features a full incubation suite for temperature and CO2 control, making it ideal for live-cell studies. Multispectral imaging is another possibility with the LSM880's native 32-channel Quasar detector and two additional PMT detectors: the entire spectrum is scanned at once to quickly build a database of relative fluorophore signal contribution from control samples, and the system can then easily separate emission signals that exhibit high spectral overlap during live imaging of multiplexed samples. DIC imaging is also possible using a transmitted PMT detector.

The LSM780 system sits on an upright Axio Examiner microscope stand with a fixed stage. It has seven laser lines (see below) and is equipped with two fluorescence PMTs, one PMT for transmitted light, and a highly sensitive GaAsP detector that can capture 32 channels simultaneously. Up to 13 images can be captured per second at 512 X 512 pixels. Linear scanning makes this microscope suitable for a variety of quantitative image measurements, such as fluorescence correlative spectroscopy. Hardware is controlled by Zeiss Zen Black software, which also incorporates some image processing options. For imaging live samples, the microscope is enclosed by a C02, 02, humidity and temperature-controlled chamber.

The Yokogawa Spinning Disk Confocal is the CoRE's solution when optical sectioning and high-speed imaging are jointly required. Built on the inverted ZEISS Axio Observer.Z1 frame and controlled by MetaMorph, the spinning disk system is a powerful tool for observing fast live-cell phenomena where cells may not grow in a monolayer, yet individual cell responses are needed, such as during drug treatments involving real-time injections.

Illumination is provided by the Vortran VersaLase laser launch, with six excitation lasers (405/445/488/514/561/642nm) for multi-color imaging. A motorized stage provides opportunities to image multiple areas of a sample automatically over time. Stage-top incubation for short-term maintenance of cell viability is also available; features include a heated stage insert with cover, humidity and CO₂control, and an objective heater ring.

Imaging is provided by the Yokogawa CSU-X1 spinning disk module and two Hamamatsu ImagEM EMCCD cameras for better low-light, rapid imaging; up to two fluorescent channels can be imaged simultaneously. On-site tissue culture equipment is also available, should researchers require it. This system also doubles as a conventional widefield microscope when coupled with the PCO.edge on the left camera port.

The Olympus FluoView FV1000MPE is a multi-photon laser scanning microscope that allows fluorescence imaging deep within specimens. It has a Coherent Chameleon Vision II laser, tunable from 680nm to 1080nm, as well as a 473nm laser diode for single photon excitation. It has four external (non-descan) detectors, as well as three confocal PMTs and one transmitted light detector. It is capable of timelapse and FRET imaging experiments. The motorized stage contains adapters for different dishes, slides, and small animals to accommodate a wide range of experimental setups, and is also capable of automated montage acquisition and stitching to generate high resolution images of large areas. Dipping lenses allow imaging directly into specimens in media.

Resources for the Olympus FV1000 MPE include:

User Protocol
Mosaic Protocol

The Olympus FluoView FVMPE-RS multiphoton microscope allows fluorescence imaging at higher depths within the specimen. The upright microscope provides space for large samples and a high degree of motorization. With its ultra-stable arch-like structure, the system offers a high degree of flexibility to suit different samples.

This tool is ideal for in vivo observation requiring maximum space. To facilitate simultaneous two-color excitation, it is equipped with Spectra-Physics Insight X3 tunable ultrafast lasers, having a dual output: tunable laser output from 690nm to 1300 nm, and the fixed laser line at 1045. In addition to the high NA 10X and 25 X objectives, the microscope is equipped with a computer-controlled correction collar system that can automatically adjust to compensate for spherical aberration during deep observation of thick samples. There are four non-descanned detectors on the microscope, two PMTs, and two GaAsP detectors. The motorized stage can be used to image from slides, dishes, and small animals. The CoRE also has an E-Z Anesthesia machine to assist in intra-vital imaging experiments.

The microscope is additionally equipped with an inner focus articulating nosepiece that can be mounted on the microscope, providing more degrees of freedom by using a movable arm while facilitating rapid axial focusing with no mechanical movement. The software aids in acquiring large mosaic tiles to image large regions. Together with all these features, the microscope can be used for high-sensitivity, high-resolution deep tissue imaging, intra-vital imaging, optogenetics, electrophysiology, label-free imaging (SHG, THG), among other applications.

Resources for the Olympus FVMPE-RS include:

User Protocol

The CellInsight CX7 LZR platform is a laser-based, high-content imaging system that automates everything from imaging to data extraction. Equipped with seven solid-state lasers (405nm, 450nm, 488nm, 561nm, 594nm, 647nm, and 785nm) and Olympus objectives (4x/10x/20x/40x/60x; highest NA=0.90), the system is capable of fast widefield imaging, spinning disk confocal imaging for improved optical sectioning, and brightfield imaging for sparse wells. Pre-calibrated sample carrier templates and fast laser autofocus minimize setup time for the user.

This instrument is used most often to image samples in glass-bottom well plates, ranging in size from 6 to 1,536 wells, but it is also compatible with standard microscope slides. The platform is integrated with ThermoFisher’s HCA Studio, a software package that enables image analysis and data extraction to be carried out concurrently with imaging, and even feeds analysis data back into the ongoing acquisition to improve results. Offline workstations can be used for additional data analysis. Users may also choose to export images and analyze them using any other software package required.

This state-of-the-art UltraMicroscope II represents the second generation of light sheet microscope developed by LaVision BioTec. The homogeneous single plane excitation is achieved by the bidirectional triple light sheet technology while the fluorescence signal is detected by a (sCMOS) camera perpendicular to the illumination plane. The selective plane illumination strategy offers excellent optical sectioning capabilities and reduces fluorophore bleaching. As a result, a 3D image stack of cleared whole-mount organs can be generated in reasonable time. UltraMicroscope II imaging is compatible with both organic solvents and aqueous buffers.

Resources for the LaVision Light Sheet Microscope include:

User Protocol

Lifecanvas SmartSPIM is an advanced light sheet microscope capable of imaging large tissue samples at high speed. Axial sweeping technology allows for generating homogenous axial PSF across the entire field of view. Illumination optics scan the beam while synchronized to the camera’s rolling shutter detection. As a result, a 3D image stack of cleared whole-mount organs can be generated (whole mouse brain with one color channel 1.625x in <10 min, 3.6x in < 45 min). Available laser lines are 488, 561, 647, and 785nm. Objective lenses with magnifications 1.65X, 3.6X, and 9X are available for imaging.

Post-processing is also available, including computational streak/stripe removal and stitching. Those interested in using this tool are encouraged to contact the CoRE to verify the clearing method and imaging buffer compatibility.

The HT7700 is a transmission electron microscope that includes Hitachi’s “dual-mode” objective lens, allowing users to achieve superior low magnification, high-contrast, and high-magnification, high-resolution imaging. All image acquisition is digital and there are options that can be used to readily examine and align serial sections. The system features a high-resolution AMT XR41-B digital camera with 2K-by-2K capability. As the fourth generation of PC-based transmission electron microscopes (TEMs), the HT7700 builds upon its predecessor, the H-7500, and exclusively utilizes digital imaging technology.

The HT7500 transmission electron microscope is equipped with a phosphor screen and an AMT NanoSprint12:12 Megapixel CMOS TEM digital camera. This system is designed for observation and evaluation of specimens using the electron beam maximum acceleration of 120 KV.

Within both the low and high magnification functions, wide fields are available. Focal distance is also selectively usable between high resolution and high contrast applications by means of a double-gap objective lens. The main PC integrally controls the TEM main unit and digital AMT camera. A secondary PC is attached, allowing the user to track and assemble serial images via image software. The H-7500 was Hitachi’s first pc-based TEM sold in the United States and includes a phosphor screen that can take pictures with film or use a digital camera.

Sectioning capabilities for the CoRE electron microcopy is provided by the UCT and UC7 ultramicrotomes. These systems are capable of section thicknesses down to 60 nanometers for ultrathin slicing; with normal sectioning being performed at 80-90nm for ultrathin slices and 0.5-1.0 micron for semi-thin slices. Epon- or lowicryl-embedded samples are sliced according to the sample type, and sections are then mounted on mesh or slot grids as appropriate. 

Training is not typically provided on this instrument but is possible, given strict approval or extensive prior experience.

Our TEM services currently include:

• Fixative/Chemical preparation
• Perfusion of large (NHP) to small animal models
• Vibratome sectioning
• Embedding
  • For morphological/ultrastructural preservation studies-Embed 812 "Epon"/Durcapan embedding- (tissue, cultured cells, suspended cells, cell fractions, viruses)
  • For Immunohistochemical studies- Freeze substitution resin embedding-Lowicryl HM20 Resin- (tissue, suspended cells)
  • High Contrast embedding for FIB-SEM/ 3View
• Ultramicrotome Sectioning
  • Semi-thick (Toluidine Blue Stain on slides- 0.5µm- 1µm thick)
  • Ultrathin- 2D (minimum 60nm-90nm)
  • Serial Sectioning for 3D volumetric studies
• Contrast Counterstaining (Uranyl Acetate and Lead Citrate)
• Pre-screening for CRYO TEM samples
  • Negative staining (e.g., viral suspension, exosomes)
  • Deionizer and carbon coater on site
• Pre-embed Immunogold labeling