1. Resources
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Microscopy and Advanced Bioimaging CoRE

Workstations and Software
Author’s Information
Rates and Policies
Sample Preparation Instructions

The Microscopy and Advanced Bioimaging CoRE is a shared resource facility that provides access to state-of-the-art imaging equipment and analysis tools. Situated within the Icahn School of Medicine at Mount Sinai, our facility is available to both internal and external users and accessible seven days a week. It houses widefield, laser scanning confocal, spinning disk confocal, multi-photon, light-sheet, and super-resolution microscopes, along with two transmission electron microscopes and a high-content screener. The CoRE also offers a high-end centralized workstation for image processing, high-performance computing capabilities, and data storage. It additionally provides access to several commercial software programs for image analysis and data quantification. 

Our facility services include consultations for sample preparation, training on the microscopes, full imaging support, and assistance with analysis strategies. Our CoRE scientists can also collaborate with investigators to develop novel imaging methods and analysis approaches. We also provide several services related to transmission electron microscopy: tissue/cell processing, image acquisition training or assistance, and image analysis support.

The Microscopy Core is an established Leica Center of Excellence, and a collaboration between the Icahn School and Leica Microsystems.  

Educational Resources

Each month, usually on the third Thursday, we host invited speakers who deliver seminars on topics relevant to imaging. These topics include both biology-driven presentations, in which speakers use imaging as a major tool in their research, and presentations from companies that have resources relevant to Mount Sinai’s investigative community. They range from probe development to new microscopes and imaging analysis technology. Throughout the year, we additionally offer workshops on focused subjects for researchers and sponsor equipment demonstrations.

Additional Information iLabs Reservation Become a Trained User Microscopy Lab Website

Meet the Microscopy and Advanced Bioimaging Team

Deanna L Benson, PhD
Deanna L Benson, PhD
PROFESSOR | Neuroscience
GUOBIN SUN
GUOBIN SUN

Senior Core Scientist

ALLISON S PORTELA
ALLISON S PORTELA

Senior Core Research Associate

Nikolaos Tzavaras, PhD
Nikolaos Tzavaras, PhD

CoRE Operations Manager, Microscopy and Advanced Bioimaging CoRE

Katarzyna Cialowicz, PhD
Katarzyna Cialowicz, PhD

Senior Scientist

William G. Janssen
William G. Janssen

Senior Scientist

Jose Javier Bravo-Cordero, PhD
Jose Javier Bravo-Cordero, PhD

Associate Professor, Medicine, Hematology and Medical Oncology

ARUN NARASIMHAN
ARUN NARASIMHAN

Senior Core Scientist

GLENN DOHERTY
GLENN DOHERTY

Senior Core Research Associate

Instruments and Services

The Microscopy and Advanced Bioimaging CoRE at the Icahn School of Medicine at Mount Sinai is dedicated to empowering researchers with advanced imaging capabilities. Whether a project demands high-speed live-cell monitoring, super-resolved nanoscale visualization, deep-tissue exploration, or electron microscopy, our instrumentation is available to support even the most ambitious projects. Staffed by a team of specialists, the CoRE is also committed to providing tailored solutions and expertise that furthers our efforts to rapidly advance biomedical discovery.

CoRE Staff will help you select and receive training on the appropriate microscope for your experiment. We maintain and operate several imaging systems, including: 

  • Widefield Microscopes  
    • ZEISS Axio Imager.Z2 (2x)  (RRID:SCR_018876) 
    • ZEISS Axio Observer (2x) (RRID:SCR_021351) 
    • Leica DMi8 (RRID:SCR_026672) 
    • Leica DM 6B (RRID:SCR_024857) 
    • Olympus MVX10 fluorescence macroscope (RRID:SCR_018612) 
    • ZEISS SteREO Lumar.V12 fluorescence macroscope  
  • Confocal Microscopes 
    • Super-resolution: Leica TCS SP8 with STED 3x and White Light Laser  
    • Super-resolution: Zeiss LSM 880 with 32-channel spectral GaAsP array + PMTs and the Airyscan detector   
    • Super-resolution: Zeiss LSM 980 with 32-channel spectral GaAsP array + PMTs + 2 NIR GaAsP detectors and the Airyscan 2 detector (RRID:SCR_025048) 
    • Leica Stellaris 8 (2x) with White Light Laser and 4 spectral Power HyD detectors 
    • Leica TCS SP8 with spectral detector, dichroic beamsplitter (RRID:SCR_018169) 
    • Leica TCS SP8 with spectral detector, AOBS beamsplitter (RRID:SCR_027226) 
    • Zeiss LSM 780 with 34-channel spectral detector  
    • Andor Dragonfly 620 spinning disk confocal with TIRF and SMLM capabilities, photostimulation (RRID:SCR_027225) 
  • Multiphoton Microscopes 
    • Olympus FVMPE-RS-with Dual Line Insight X3 laser (RRID:SCR_027234) 
    • Bruker Ultima 2Pplus with Coherent Chameleon Discovery NX Dual Laser Line 
  • Lightsheet Microscopes  
    • LifeCanvas SmartSPIM (RRID:SCR_027239) 
    • LaVision Biotec UltraMicroscope II (zoom and infinity optics available) (RRID:SCR_027238) 
  • High-Content Screeners 
    • Agilent Cytation C10 with Biotek Biospa 8 
    • ThermoFisher CX7 LZR (RRID:SCR_020546) 
  • Transmission Electron Microscopes  
    • Hitachi 7500
    • Hitachi 7700 (RRID:SCR_020022) 

CoRE Staff have methodically condensed the most up-to-date sample preparation techniques for microscopy into a series of presentations. Contact the CoRE directly for copies of this material and/or to have a discussion about current issues you are facing. 

  • Basic Light Microscopy Sample Preparation 
  • Lightsheet Sample Preparation 
  • STED (super-resolution) Sample Preparation 
  • SMLM (super-resolution) Sample Preparation 
  • Guide for Using Multi-Area Carriers (well plates, chambered coverglass, etc.) 
  • The MABC hosts a number of servers and computer workstations equipped with a variety of open-source and commercial image analysis software.

Servers and Workstations

    • Bruker (previously Acquifer) HIVE - for file transfer and pre-processing of large data sets, 3D visualization 
    • Microscopy HPC - for analysis of extremely large data sets
    • Two terminal workstations for dedicated image analysis
    • Linux server for dedicated ClearMap analysis 

Software Packages on which users can be trained and receive access: 

    • FIJI/ImageJ 
    • Bitplane Imaris 
    • AIVIA 
    • Arivis Pro and Cloud 
    • QuPath 
    • CellProfiler 
    • Huygens Professional 
    • Leica LAS X - FLIM analysis
  • Custom software can be installed after discussion with, and at the discretion of, CoRE Staff. Please reach out for assistance.
  • Scripting languages and environments available on servers: 
    • Anaconda  
    • MATLAB 
    • R 
    • Python