[Skip to Content]

Neuroscience Microscopy Core

Core: Neuroscience Microscopy Core
Core Director: Arvydas Matiukas, PhD
Phone: 315 464-7997
Location: 3607 IHP/NRB
Email: [email protected]

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 Core provides instruments to image fixed samples and live cells. The hardware and software allow different imaging modes ranging from single slice to multicolor 3D time series, and large area tiling. Available environmental chamber provides optimal conditions for long term experiments on live cells.

Project consultation/collaboration, training, and technical assistance are available from Core Director (a Zeiss certified microscopy specialist). All users must receive training (separate for each microscope) before operating the equipment. Trained and proficiency certified users may operate the Core equipment without supervision.

Instrumentation in Core

Zeiss LSM 780 confocal reservation calendar
The LSM780 is an inverted microscope with 4 lasers, 3 detectors, an environmental chamber, and mercury and halogen light sources. The microscope has 6 excitation color capabilities, and 3 independent fluorescence imaging channels including one spectral, and one transmission PMT. The system is configurable for simultaneous and/or sequential multicolor acquisition.


Leica SP8 with STED reservation calendar 


Confocal Microscopy 
Leica's SP8 confocal system with five spectral detector channels: two PMTs and three HyDs and HyVolution software that combines super-sensitive HyD detection with SVI Huygens deconvolution, allowing lateral resolution down to 140 nm compared with 200-250 nm for standard confocal microscopy. Excitation is provided by 405nm laser and White Light Laser (470-670nm continuous spectrum, up to 8 lines may be combined).

STED (stimulated emission depletion) 
3X nanoscopy is a super-resolution technique that overcomes diffraction limited resolution. With multiple STED laser lines of at 592 nm, 660 nm and the pulsed laser at 775 nm, STED can reach a resolution below 30 nm.

Digital light sheet (DLS) Microscopy (currently not online)
DLS microscopy is a fluorescence technique that uses a plane of light for 3-D imaging that is useful for large samples such as embryos, sensitive samples, or fast biological processes in vivo. It provides good optical sectioning capabilities and high speed with low levels of photobleaching.


Deconvolution workstation with Huygens software
Huygens software restores 2D and 3D microscopy images or time series for visualization. The restoration is based on different deconvolution algorithms, that permit the recovery of original objects/structures from their confocal images that were degraded by blurring and noise. Deconvolution significantly increases image contrast and improves resolution (about 2x in Z and about 1.5x in XY).


Facility Rules

If you fail to show up for time you have scheduled on the calendar, you will be billed for the amount of time scheduled 

Removal (cancellation) or modification of time scheduled on the calendar must be done at least 24 hr before the time you were scheduled for or you will be billed for the amount of time originally scheduled.

New user enrollment:

  • The new user downloads and completes the Enrollment Form, emails it to Arvydas.
  • Staff coordinates and schedules training date and time.
  • More training sessions are scheduled as needed to complete training.
  • The new user is granted status and access corresponding to their training.
  • Always remember to acknowledge the use of Core microscopes and/or staff assistance to generate images/data in your publications.



  • All users must be trained before they are allowed to use the microscopes. After training, an account will be set up for reserving time and using the microscope.
  • All users must sign up on the online calendar to reserve time before use of the microscopes, and record actual usage in paper log.
  • Users must clean the microscope objectives they used and dispose of garbage when finish. If you bring any live specimens or potentially harmful samples, please dispose of them in your lab.
  • Please check the online booking calendar at the end of your session to facilitate last minute changes and scheduling updates. Leave the system on if someone is reserved next within two hours; keep the lasers in standby whenever possible to prolong their life.
  • The last user of the evening is responsible for shutting down the microscope system.
  • You are responsible for your data. The system computers are for temporary image storage. Please save your data on the data hard drive of the computer and transfer your image data as soon as possible after acquisition. Image files left on the computer hard drives will be subject to periodic removal.
  • Users are required to report any problems or damages during usage of the microscope.
  • No food or drink is allowed in the microscope rooms.


  • The hours billed are based on your computer log off. Remember to log off to end the billing session.
  • All users must record system usage on the paper log at each microscope.
  • Minimum time billed is 1 hr 
  • Each imaging session will be billed by the larger of either the time reserved or hours used in 1 hr increments (i.e., all time is round up to a full hour)
  • After the first 6 hours of training you will be charged for both training and laser usage
  • Technical support is billed in 1 min increments and added to the cost/hr for the laser usage
  • There is a quarterly cap on the cost of laser use. Other fees (training, technical support etc) are billed in addition to laser use and are not discounted.
  • If you fail to show up for time you have scheduled on the calendar, you will be billed for the amount of time scheduled (this is not considered laser use and is not included in the quarterly discount).

Removal (cancellation) or modification of time scheduled on the calendar must be done at least 24 hr before the time you were scheduled for or you will be billed for the amount of time originally scheduled. (Note the calendar keeps electronic record of all entries and modifications).

Calendar Sign up:

  • All calendar reservations are in 1 hr blocks
  • Advance reservation is limited:
    • starting Friday of each week ONLY TIME FOR THE NEXT WEEK may be booked
    • there is a limit of 5 hrs/weekday/lab booking that should fit into either 8am-1pm or 1-6pm window (in 1 hr blocks)
  • If time is available, you may sign up in the afternoon for additional time, only for the next day (in 1 hr blocks).
  • Time reserved on weekends and off hours is not limited in duration, but you may only sign up (starting Friday) for the following week.
  • If you finish early contact the next user before turning off the laser.
  • Specific for the Leica - when signing up on the calendar specify the modality you will use. If you need specific objectives contact the core director ([email protected]) when you sign up.

Videos and resources

Videos/resources on fluorescence microscopy and confocal microscopy:

Good Resources

JoVE (wide field, basics of fluorescence microscopy of samples)


Microcourses from Harvard


iBiology Microscopy courses


Recommended for fluorescence microscopy and confocal overviews






Preventing Damage

Preventing lens damage:
Preventing Objective Lens Damage: Blunt Force Trauma


Immersion Oil Problems


Microscopy Course on iBiology

Popular, free online microscopy course begins with basics of optics, proceeds through transmitted light microscopy, and covers many microscopy methods.



Neuroscience Microscopy Core Fee Schedule


Download forms and protocol

New user Enrollment Form


More Information

SUNY Upstate Medical University and Leica Microsystems, Inc. have combined efforts to establish the Leica Microsystems Center of Excellence at SUNY Upstate. The Center supports a mission to drive new discoveries and insights from scientific research performed using state-of-the-art imaging systems.