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Advanced Light Microscopy Core Laboratory


This lab offers research scientists access to high-end instrumentation for fluorescence microscopy. We offer support with image acquisition, processing, analysis and presentation.





  • Applied Precision SoftWorx Workstation ( Acquisition computer )

  • Bitplane Imaris workstation ( Computer cluster )

  • Deltavision CoreDV Widefield Deconvolution System ( Deconvolution microscope )

    "The Deltavision CoreDV Widefield Deconvolution System is a high resolution widefield microscope for acquiring images of live or fixed samples. The system is built on an Olympus IX71 inverted microscope and features an LED transmitted light source for differential interference contrast and a 7-color solid state illumination unit for exciting fluorophores across the visible spectrum. Polychroic beam splitters, optimized for imaging with Blue-Green-Red-FarRed fluorophore combinations in fixed cells or CFP/YFP and GFP/RFP combinations of expressed proteins in living cells, are combined with emission switching through fast filter wheels. Images are captured on a Nikon CoolPix HQ cooled CCD camera. The motorized stage is controlled by XYZ nanomotors for accurate z-stack and point-visiting functions."

  • IncuCyte Zoom ( Incubator microscope )

    The IncuCyte ZOOM is an imaging device that sits in a tissue culture incubator and takes time-lapse images of cells in phase and red and green fluorescence. The device is particularly suited for monitoring cell growth and migration. A variety of culture vessels are accommodated in this device. Conveniently, captured image data is accessible from any computer on OHSU’s intranet.

  • MetaMorph workstation ( Computer cluster )

  • Nikon Yokogawa CSU-W1 spinning-disk confocal microscope ( Spinning-disk confocal microscope )

    "This setup is custom-built around a Yokogawa W1 spinning disk confocal head mounted on a Nikon Ti inverted microscope with PFS attachment for continuous Z-drift compensation during live-cell imaging. This is a four color system (405nm, 488nm, 561nm, and 631nm). X,Y,Z axes are motorized to allow for position marking and revisiting during long-term timelapse recordings. A Piezo-driven Z axis top plate allows for fast Z stack acquisition with all available objectives. Objectives range from low magnification dry objectives to high NA oil immersion objectives. The system has full environmental control for live-cell imaging."

  • Olympus FV1000 laser scanning confocal microscope ( Laser scanning confocal microscope )

    "This laser scanning confocal is mounted on a fully motorized BX-71 upright microscope base. The stage is motorized in X,Y to mark positions for revisiting or stitching neighboring field-of-views into a single image. The strength of this system is its upright stand configuration that allows samples to be imaged from the top using dipping objectives."

  • Zeiss Apotome wide-field microscope ( Stereo microscope )

    The Zeiss Apotome setup is a wide-field microscope setup with a choice of a black-and-white or a color CCD camera for fluorescence- or colorimetric-based immunohistological detection. The Apotome device captures optically sectioned images from thin tissue sections more efficiently than a laser-scanning confocal microscope. The setup is equipped with a motorized x,y stage that can be used to stitch images across a piece of tissue larger than the field-of-view captured in a single image.

  • Zeiss Elyra PS.1/LSM 710 Super-Resolution system ( super-resolution microscope )

    The Zeiss Elyra PS.1 setup implements two different super-resolution technologies. It is capable of structured illumination microscopy, which can improve resolution 2-fold in each dimension, or 8-fold in volume. This technology uses labeling procedures commonly used for laser-scanning confocal microscopy and direct comparison of confocal and super-resolution imaging is possible on the combination setup. The system is also capable of single-molecule localization microscopy, a specialized super-resolution method that achieves almost 10-fold improvement in resolution in x and y.

  • Zeiss LSM 780 laser scanning confocal microscope ( Laser scanning confocal microscope )

    "The Zeiss LSM780 is mounted on a fully motorized AxioObserver Z1 inverted microscope stand. The stage is motorized in X,Y to mark positions or acquire images of areas larger than the field of view through tiling of individual image stacks. An optional stage-top incubator is available to control temperature and atmosphere and a Definite Focus attachment compensates for slightest Z-drifts during live-cell timelapse imaging."


  • Dendra2 conversion protocol ( Protocol )

    "This protocol is provided for use with the pDendra2 Vectors which encode a green-to-red photoswitchable fluorescent protein derived from the octocoral Dendronephthya sp. Dendra2 switches irreversibly from green to red when exposed to intense 405 or 488 nm light."



  • Imaris ( Software )

    "Imaris is Bitplane’s core scientific software module that delivers all the necessary functionality for data visualization, analysis, segmentation and interpretation of 3D and 4D microscopy datasets. Combining speed, precision and ease-of-use, Imaris provides a complete set of features for working with three- and four-dimensional multi-channel images of any size, from a few megabytes to multiple gigabytes in size. Conveniently load, process and visualize data and images acquired from almost any confocal and wide field microscope to gain new and groundbreaking insight from your image data."

  • MetaMorph ( Software )

    "MetaMorph® Microscopy Automation & Image Analysis Software is the industry standard for automated microscope acquisition, device control, and image analysis, bringing microscopists greater understanding of cell morphology, function, and behavior."

  • softWoRx ( Software )

    "softWoRx® is the latest in DeltaVision image acquisition software. Find samples, acquire images and process data quickly and efficiently with the intuitive user interface. softWoRx 5.0 includes visualization and measurement tools and exports data in a wide variety of formats making it a versatile tool for more than just image acquisition."

  • ZEN software ( Software )

    "ZEISS Efficient Navigation (ZEN) is the single user interface you will see on all light microscopy imaging systems from Carl Zeiss. ZEN microscope software leads you simply and quickly to the result. At all times you see which options the system is making available to you and which step is appropriate to take next. Use ZEN imaging software to achieve scientific success: nothing diverts you from your goal - to document your results and reproduce them at any time."

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Last updated: 2012-07-16T15:11:38.763-05:00

Copyright © 2016 by the President and Fellows of Harvard College
The eagle-i Consortium is supported by NIH Grant #5U24RR029825-02 / Copyright 2016