Confocal and Two-Photon Imaging

Zeiss Confocal
Core: Confocal and Two-Photon Imaging Core
Core Director: Arvydas Matiukas, PhD
Phone: 315 464-7997
Location: 3163 Weiskotten Hall

Instrumentation in Core:

  • Zeiss LSM510 scanning confocal/two-photon microscope system
    reservation calendar
  • Zeiss LSM 780 confocal
    reservation calendar
  • Deep Brain 2p Imaging Microscope
    reservation calendar
  • Superresolution Microscope
    reservation calendar
  • Environmental chamber providing temperature and CO2 control
  • Coherent Chameleon tunable phased NIR laser for two-photon excitation
  • Newport vibration isolation optical table
  • A separate graphical workstation with Zeiss and ImageJ software for image analysis

Brief Description of Core: This core facility enables neuroscientists to visualize the structure of individual neurons and their activity in the living organism and has potential applications in many other research areas (such as microbiology, molecular biology, ophthalmology, etc.) for the study of 3D structure and process dynamics.

The microscope system consists of two microscopes (inverted and upright) that share a portable scanhead with multiphoton excitation imaging and spectral detector capabilities. Three independent simultaneous confocal channels for reflection and fluorescence are available as well as fourth channel for transmission (DIC) imaging. Wide variety of objectives, digital zoom, and motorized stage allow imaging broad range of specimens: from individual cell to 10cm piece of tissue.

This system employs a PC-based user interface to control the microscope, laser excitation, scanning and image acquisition, and is capable of digitally capturing up to 12-bit 2,048x2,048 images, while the LSM 5 Software controls image data acquisition, presentation, processing, and archiving, with 3D image reconstruction and multiple time series features also available. The software along with image saves whole experiment configuration thus simplifying long/repetitive experiments.

Project consultation, training, and technical assistance are available from Core Director (a Zeiss certified microscopy specialist). Trained users can use the Core equipment for self service imaging.

Core Fee Schedule:

Training and assessment (new users, 10hrs)


Prime time usage (Mon-Fri, 7am-7pm)


Off-prime time usage


External users (non-Upstate)


Technical support


Billing Rules:
Minimum time billed is 1 hr
After the first hour usage is billed in 30 min increments
Training and technical support are billed in 1 min increments

How to Access Core Services: Phone or email.

The Core will be moved to the new Neuroscience Research Building and expanded in March 2014. A few weeks downtime is projected (March 10-31). Check for updated information, including fees after March 31, 2014.

Replacement confocal (Nikon C2, 3 color blue/green/red) is available in WH (currently there is no user fee for the Nikon C2). A new user has to obtain free basic training from Dr. Matiukas prior to using this confocal. Please request the training in advance (1 week at least) and before March 2014.