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Neuroscience Microscopy Core

Core: Neuroscience Microscopy Core
Core Director: Arvydas Matiukas, PhD
Phone: 315 464-7997
Location: 3607 IHP/NRB
Email: matiukaa@upstate.edu

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 was moved to the new Neuroscience Research Building and expanded in 2014. 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 LSM510 scanning confocal/two-photon microscope system
    Off line as of July 2018. An S10 equipment grant for a replacement Confocal has been submitted.

  • 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.
    Lasers: a 405nm solid state violet laser, a multiline (458, 488, 514nm) Ar laser, a 561nm solid state yellow laser, and a 633nm HeNe red laser.
    Detectors: highest sensitivity GaAsP detectors and two highly sensitive low dark noise PMTs

  • 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).


Neuroscience Microscopy Core Fee Schedule


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Calendar sign up

All calendar reservations are now in 1 hr blocks
Advance reservation is limited:

  1. a) starting Friday of each week ONLY TIME FOR THE NEXT WEEK may be booked
  2. b) 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.

Billing rules

  • 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)
  • Technical support is billed in 1 min increments and added to the cost/hr for the laser usage
  • The annual power user fee has been replaced by the quarterly discount. There is now 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).

How to Access Core Services

Phone: 315 464-7997
Email: matiukaa@upstate.edu

If any user has difficulty accessing the LSM780 confocal or has a project that does not fit into the new rules please contact Core Director Arvydas.

The Core is housed in the Neuroscience Research Building (NRB).

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