Microscopy & Image Analysis Workstations



We are currently operating according to policies described in our approved Stage 1 Recovery Plan.

A summary of these policies is posted up around the core, as well as HERE.



CLICK HERE to get answers to our most frequently asked COVID-19 operational status questions.



We have had an increasing number of requests for the retrieval of old sequencing data from our archive. While we are always happy to help whenever we can, a couple of issues have arisen surrounding this. CLICK HERE to review our new policy on data retention & retrieval.


If you are new to the core or microscopy and would like guidance with choosing which instrument would best suit your experiment, please email Adam Fries at afries2@uoregon.edu, drop by my office in Klamath Hall room 270D, or fill out a Microscopy Consultation Form.


The Core currently offers training and support for the following microscopes:

Leica SPE Laser Scanning Confocal and Widefield

  • 405nm, 488nm, 561nm, 633nm laser excitation lines, and DIC illumination
  • DAPI, FITC, TRITC equivalent for widefield imaging
  • Motorized stage, upright body
  • 5x, 10x, 25x water dipping, 40x oil, 40x water dipping, 63x oil objectives
  • Acquisition software is LAS X on Windows 10
  • Usage Rates - Internal (UO, OSU, OHSU): $20/hr, External $40/hr
















Cytiva DeltaVision Ultra - Widefield with Deconvolution

  • LED excitation lines of 405nm, 458nm, 488nm, 514nm, 555nm, 594nm, 633nm
  • 20x LWD, 20x, 60x oil, 100x oil objectives
  • Motorized stage, pco.edge sCMOS camera, inverted body
  • Acquisition software is Acquire Ultra on Linux CentOS 7
  • Usage Rates - Internal (UO, OSU, OHSU): $20/hr, External: $40/hr















Zeiss LSM 880 with Elyra Structured Illumination and Airy Scanning

  • 405nm, 458nm, 488nm, 514nm, 561nm, 633nm laser excitation lines
  • 10x, 20x, 40x water immersion, 40x oil, 63x oil objectives
  • Motorized stage, light-tight enclosure, inverted body
  • Acquisition Software is Zen Black on Windows 7
  • Usage Rates - Internal (UO, OSU, OHSU): $35/hr, External: $70/hr















Nikon CSU-W1 SoRa Spinning Disk

  • Spinning Disk excitation lines are 405nm, 488nm, 561nm, 633nm, and DIC illumination
  • TIRF imaging with excitation lines of 488nm, 561nm, and 633nm
  • Digitial Multi-Mirror Device and Lumencor Spectra X for photo-stimulation with LED stimulation lines of 390nm, 440nm, 488nm, 561nm, 594nm, 633nm, 740nm
  • 405nm photobleaching laser line
  • 4x, 10x, 20x, 40x water immersion, 60x water immersion, 60x oil TIRF objectives
  • Motorized stage, dual Prime BSI sCMOS cameras for optional simultaneous green/red imaging, inverted body
  • Acquisition sofware is Nikon Elements + JOBs on Windows 10
  • Usage Rates - Internal (UO, OSU, OHSU): $35/hr, External $70/hr














Support and training will exist in the near future for:

  • Custom-built Light Sheet microscope
















The Core currently has 4 analysis workstations and include the following software:

(Usage Rates - Internal (UO, OSU, OHSU): $25/hr, External $50/hr)

  • Imaris 9.9 with Cell and Filaments Modules
  • Imaris 9.9 Converter and Stitcher
  • Prism8
  • Matlab 2018a
  • Adobe Illustrator and Photoshop
  • Microsoft Office
  • Zen Blue/Black
  • Python3
  • FIJI

Calendar Access and Training:

  • Instrument reservations are made though iLab and each user will need to register an iLab account if they do not have one. Once training on the instrument has been scheduled and completed, new users will be granted calendar access.


  • Individualized training recharge for each of the instruments is a onetime fee of $150 ($300 for external customers).


  • Contact Adam Fries afries2@uoregon.edu for more information regarding instruments, training, or analysis. Or visit the office in Klamath 270D.





(If you have urgent microscopy-related questions in the meantime, please email afries2@uoregon.edu or dturnbul@uoregon.edu)