Scheduling is online. Check what's open this week and book time on the Krios, Arctica, Aquilos and plunge freezers.

Book instrument time New user? Request an account

Institute for Quantitative Biomedicine · Rutgers University

Rutgers CryoEM & Nanoimaging Facility

The Rutgers CryoEM & Nanoimaging Facility (RCNF) specializes in high-resolution imaging of purified proteins, macromolecular complexes and cells, preserved in their native state by vitrification. The RCNF also supports materials science research.

Book instrument time Email us

Proteomics Building, Busch Campus, Piscataway NJ

Plunge freezer in the RCNF sample prep area — Plunge freezer in our prep area

4electron microscopes (two TEMs, SEM, FIB/SEM)

1.84 Åbest resolution so far

2020Aquilos 2 installed, the first in North America

Opento Rutgers and external users, fee-for-use

About the facility

The RCNF preserves biological specimens in their native state by vitrification; images them at the nanoscale through cryo-transmission electron microscopy, cryo-scanning electron microscopy, or cryo-focused ion beam microscopy; and reconstructs three-dimensional information through computational analysis of these nanoscale images.

We currently operate four electron microscopes: two cryo-transmission electron microscopes (a 300 kV Titan Krios and a 200 kV Talos Arctica), a cryo-scanning electron microscope, and cryo-focused ion beam/scanning electron microscope. Our cryogenic light microscope allows multimodal correlation. Additional equipment includes Leica ACE600 rotary shadower (for e-beam deposition of platinum or carbon) and plunge-freezers: FEI Vitrobot Mark IV, and Leica EM-GP.

Most projects will begin with a scoping consultation with facility staff. We aim to foster the development of expert cryo-electron microscopists across all Rutgers campuses. The RCNF is also open to external users with particular emphasis on the biotechnology industry.

We changed our name from the Rutgers New Jersey Cryo-Electron Microscopy and Tomography Core Facility in October 2020 to reflect the diversity of imaging techniques employed in the facility.

Loading a sample cassette into a cryo instrument

Gloved hands holding a liquid-nitrogen grid transfer station

Researcher at the cryo-correlative light microscope

The Synergy sculpture outside the Proteomics Building at night

Part of the Institute for Quantitative Biomedicine

The RCNF is a core facility of the Rutgers Institute for Quantitative Biomedicine (IQB). IQB was founded in 2015 by Stephen K. Burley, M.D., D.Phil., who also directs the RCSB Protein Data Bank.

IQB is based in the Proteomics Building on Busch Campus. We're on the ground floor, next to the high-field NMR and biological mass spectrometry facilities.

More about IQB

Instruments

Krios Talos Arctica FIB/SEM CLEM SEM Sample prep

Inside the RCNF Titan Krios column, with the autoloader and cassette controls on the left

Cryo-transmission electron microscope

Thermo Fisher Titan Krios, 300 kV

X-FEG
BioQuantum energy filter
K3 detector
±70° tilt
Single particle
Tomography
MicroED

The Krios is our 300 kV microscope for high-resolution single-particle cryo-EM and cryo-electron tomography, and it can also be used for microED. It has a high-brightness X-FEG electron source, a Gatan BioQuantum energy filter and a K3 direct electron detector. The stage is stable at cryogenic temperatures and tilts to ±70° for tomography, and the higher voltage makes it better suited to thicker specimens than the Talos Arctica.

Get in touch to talk about access and scheduling.

Cryo-transmission electron microscope

Thermo Fisher (FEI) Talos Arctica, 200 kV

BioQuantum GIF
Volta phase plate
Summit K2 detector
12-sample autoloader
SerialEM
2.5 Å SPA
±70° tilt

For single-particle reconstruction of protein complexes and for cryoelectron tomography, we image around the clock on our 200 kilovolt Talos Arctica cryogenic transmission electron microscope. It is equipped with a BioQuantum Gatan Image Filter to remove inelastically scattered electrons, a Volta phase plate for contrast enhancement, and a Summit K2 direct electron detector for optimal detector performance at high resolution. This configuration is suitable for both single-particle and tomographic studies. The instrument is piloted remotely from an adjoining control room (or over the 'net) outfitted with automated collection software such as SerialEM. Using aberration-free image shift, with a good specimen the TEM can collect thousands of images per day and can produce single-particle reconstructions at 2.5Å resolution. Batch tilt-series for tomographic reconstruction can be collected with 140° tilt range.

The Talos Arctica is operated at a constant stage temperature of 79 K. All samples are introduced via the "autoloader" 12-sample-handling robot. Facility staff load samples to the autoloader and perform instrument alignments. Because of the nature of experiments on the Arctica, the minimum reservation time is one day, during which we expect at least 16 hours of instrument use will be possible. In-depth training is available and encouraged for scientists who anticipate recurring use of the instrumentation.

Thermo Fisher Aquilos 2 cryo-focused ion beam scanning electron microscope

Cryo-focused ion beam / SEM

Thermo Fisher Aquilos 2

Gallium FIB
EasyLift nanomanipulator
Lamella milling
Serial-section imaging
Lift-out
360°+ rotation

Rutgers was the first site on the continent to receive a ThermoFisher Aquilos 2 cryoFIB/SEM, installed in 2020. This gallium focused ion beam instrument is designed specifically for operations with cells in amorphous ice. The Aquilos 2 includes in-chamber Magnetron sputter-coater, organoplatinum gas injection system, two in-chamber and two in-column detectors, and endless 360°+ rotation. The EasyLift nanomanipulator is designed for lift-out operations. Both parallel on-grid lamella milling and serial-section imaging are facilitated with automation software. The most common use of this instrument is cutting <200nm-thick lamellae to prepare cell interior for cryo-electron tomography in the Talos Arctica cryoTEM. It is also used to perform serial section imaging by ablating a few nanometers of material at a time between SEM images, or to mill bits of tissue for lift-out cryoTEM preparation.

The Aquilos can be used at room temperature or cryogenic temperatures. Materials science samples are accepted as well as biological samples. Note that the cryostage is integrated and cannot be removed, although it can be run at room temperature. Also, to maintain the highest cleanliness of the chamber, facility policy is that all specimens be inserted and removed through the airlock, even during room-temperature operation. Overnight cryogenic runs are practical. For applications where use of the ion beam is not required, we recommend the cryoSEM. Use of the cryoFIB/SEM is priced by the hour, with daily charges capped at 8 hours for long runs.

Researcher using the Leica cryo-CLEM widefield fluorescence microscope

Correlative light & electron microscopy

Leica EM Cryo CLEM (DM6 FS)

Widefield fluorescence
Cryostage
Autogrid compatible
Z-stack montaging

To correlate image data collected by cryoEM with image data collected by optical microscopy, it is typically necessary to perform the optical microscopy at liquid nitrogen temperatures after specimen vitrification into amorphous ice. RCNF's Leica EM CryoCLEM is a widefield fluorescence microscope with a cryostage and cryotransfer shuttle that are specially constructed to hold TEM grids or Autogrids. Automated collection software facilitates whole-grid multi-channel Z-stack montaging. Correlative microscopy software installed on RCNF's cryoTEM and cryoFIB/SEM is used to relate multimodal datasets together during collection.

After vitrifying a sample on an electron microscopy grid, the same grid can be imaged in fluorescence (or brightfield) optical microscopy and in the cryoelectron microscope. Fiducial markers seen in both optical and electron microscopy are used to correlate the images. In one embodiment, a quick scan of the grid by optical microscopy is used to locate a rare event, and the user tracks the electron microscope stage to the correct site to record a tomogram or mill a lamella at that location.

LEO 1525 field-emission scanning electron microscope with Gatan Alto cryo system

Cryo-SEM micrograph of cells on a surface

Cryo-scanning electron microscope

LEO 1525 FEG-SEM with Gatan Alto 2500

Gemini column
<2 nm resolution
Freeze-etch
Sputter coating
EDS mapping

This instrument incorporates cryogenic capabilities and elemental analysis into a robust platform with high-resolution optics. The LEO 1525 scanning electron microscope is built around the Gemini crossover-free SEM column, attaining <2nm resolution at ambient temperature. Even voltages under 500 V are tractable. The system is also equipped with a Gatan Alto 2500 cryogenic system, which includes a turbopumped cryotransfer station, liquid nitrogen-cooled cryo-prep chamber for freeze-etch with Peltier-heated stage, gas-cooled integrated cryostage, and argon-fed sputter coater. The ThermoNoran "System Six" energy-dispersive X-ray spectrometry unit can provide elemental mapping for correlation with the electron image. Due to the poor signal of the in-lens detector, we recommend the in-chamber secondary electron detector be used for all imaging with this unit.

The cryoSEM is easy to learn and competitively priced by the hour. We thank the Center for Advanced Biotechnology and Medicine (CABM) for their assistance in installing this instrument; fees are waived for researchers from that unit. The cryostage is removable and can be replaced with a room-temperature stage in <5 minutes. The policies for this instrument are more liberal than for the cryoFIB/SEM: we do permit large, room-temperature specimens to be introduced through the chamber door of this instrument, bypassing the airlock.

Vitrification

Vitrification by plunge-freezing is achieved with a Leica EM-GP plunge freezer, capable of front- or back-blotting, or with a Vitrobot Mark IV dual-blotting plunger. Plunge freezers generate an aqueous layer of reproducible thickness across the EM grid and rapidly chill this layer to an amorphous, solid state. The EM-GP is ideal for cell studies and also creates uniform-thickness ice for single-particle work. We stock standard grid styles and have a Pelco EasiGlow available for hydrophilization.

Coating & shadowing

For room-temperature preparation, a Leica ACE600 electron beam deposition unit can spray ultrathin metallic platinum or carbon in coating or low-angle rotary shadowing experiments.

Computing

We've partnered with the Office of Advanced Research Computing to maintain a university-wide installation of certain cryoEM software on the Amarel cluster. Contact the director for further details. The facility maintains some resources for data processing in-house on a buy-in basis.

Using the facility

The facility is available on a fee-for-use basis, with preference in scheduling and pricing to members of the Rutgers community. We also work with users from other universities, government labs and companies.

If you're new to cryo-EM, that's fine. Send us an email with a few lines about your sample and what you're hoping to learn, and we'll set up a time to talk it through. Most projects start that way.

Talk to us

We'll go over your sample and whether cryo-EM is the right fit.

Make grids

We freeze samples on the Vitrobot Mark IV or Leica EM-GP and check the ice.

Collect data

On the Krios, the Talos Arctica, the Aquilos 2 or the cryoSEM, depending on the project.

Process

On the Amarel cluster or our in-house machines. We can train you to do it yourself.

Before you bring a sample

Before bringing a specimen to the facility for cryoTEM, users should provide supporting data that their specimen is of a suitable concentration (generally, 0.2–1 mg/mL), suitable buffer composition, and of sufficient purity for cryo-electron microscopy.

Cryo-TEM

Minimum reservation of one day (≥16 h of instrument use expected). Staff load samples and perform alignments.

Cryo-FIB/SEM

Priced by the hour, daily charges capped at 8 hours. All specimens go through the airlock.

Cryo-SEM

Easy to learn and priced by the hour. Fees waived for CABM researchers.

Ready to book?

Certified users book directly. Everyone else can book an assisted session, and new users start by requesting an account.

Book instrument time Request an account

People

Director · Associate Professor of Professional Practice

Mark Ebrahim

Mark Ebrahim is the director of the RCNF and an associate professor of professional practice at Rutgers.

Before coming to Rutgers, Mark was the head of the Evelyn Gruss Lipper Cryo-Electron Microscopy Resource Center at The Rockefeller University. Prior to that he was a senior engineer at FEI Company (now part of Thermo Fisher Scientific).

Mark is also the founder and CEO of SubAngstrom, which makes tools and provides services for cryo-EM labs. He has invented various products that serve the cryo-EM community and consulted for cryo-EM facilities all over the world.

Staff Scientist

Ashley D. Bernstein

Ashley Bernstein has been a staff scientist in the RCNF since 2024. She handles vitrification, data collection and data processing, and looks after samples from external academic and industry users.

Postdoctoral Researcher

Karen Fisher

Karen Fisher is a postdoctoral researcher in the RCNF. She helps oversee day-to-day operations at the RCNF and is responsible for operations and training on our Aquilos FIB/SEM.

Cryo-EM at Rutgers

The research interests of several members of the Institute for Quantitative Biomedicine include structural biology generally or cryo-electron microscopy techniques. These Rutgers labs use cryo-EM and related structural methods in their research.

Arnold LabCenter for Advanced Biotechnology and Medicine. Structure-based drug design against HIV and other viruses. The group's HIV reverse transcriptase structures helped lead to the drugs etravirine and rilpivirine. Dai LabCell Biology and Neuroscience and IQB. Uses cryo-electron tomography, correlative light and electron microscopy, and cryo-FIB milling to study disordered proteins and membrane complexes inside cells, with a focus on neurodegenerative disease. Deaconescu LabInstitute for Quantitative Biomedicine. Structural biology of bacterial stress responses, including how RpoS and the transcription-repair coupling factor Mfd control transcription and DNA repair. Ebright LabWaksman Institute and Chemistry and Chemical Biology. Structure, mechanism and regulation of bacterial transcription complexes, and new antibacterial and antituberculosis drugs that target RNA polymerase. Kaelber LabMolecular Biology and Biochemistry. Structural virology of small and ssDNA viruses: how they enter cells, assemble and package their genomes, plus structure-based engineering of improved gene therapy vectors. Kulczyk LabBiochemistry and Microbiology and IQB. Combines single-particle cryo-EM, single-molecule methods and correlative light and electron microscopy to study DNA replication and repair in human mitochondria, and how laminin networks in tissue are assembled and broken down. Mickolajczyk LabRWJMS Biochemistry and Molecular Biology. Single-molecule biophysics of the ATP-driven motor proteins that build ribosomes, using optical and magnetic tweezers and FRET. Neiditch LabNJMS Microbiology, Biochemistry and Molecular Genetics. Structural mechanisms of bacterial signaling, including quorum sensing, and structure-function work toward new tuberculosis drugs, using X-ray crystallography and cryo-EM. Patel LabRWJMS Biochemistry and Molecular Biology. How human mitochondrial DNA is replicated and transcribed, including cryo-EM structures of the mitochondrial RNA polymerase, and how innate immune sensors recognize RNA viruses. Petrou LabNJMS Microbiology, Biochemistry and Molecular Genetics. Single-particle cryo-EM of membrane proteins, especially bacterial membrane enzymes involved in antibiotic resistance, and receptors and ion channels relevant to human health.

Cryoelectron microscopy is complementary to classical electron imaging techniques such as classical transmission electron microscopy. The Core Imaging Lab, a unit of the Robert Wood Johnson Medical School Department of Pathology, provides services such as TEM of stained or sectioned samples to the Rutgers community.

RCNF publications on PubMed Mass Spectrometry Core NMR Facility Super-Resolution Microscopy SEBS Facilities CINJ Core Facilities EOHSI Core Facilities All Rutgers core facilities

Contact

Questions about a project, pricing or training? Email us, or stop by if you're in the building.

rcnf@iqb.rutgers.edu

Email: rcnf@iqb.rutgers.edu
Location: Ground floor, Proteomics Building
Institute for Quantitative Biomedicine
174 Frelinghuysen Road, Busch Campus
Piscataway, NJ 08854
Parking: GPS for Lots A, B or C: 679 Hoes Lane West, Piscataway, NJ 08854. Directions & visitor parking
IQB phone: 848-445-0103