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Neurobiology Imaging Facility (HMS)

Location: Harvard Medical School, Goldenson Building 242, Boston, MA 02115


The Neurobiology Imaging Facility is the Neurobiology Department core facility for light microscopy.

Our mission is to advance research by providing services in optical imaging, introducing new optical imaging equipment, providing learning opportunities to researchers in the Longwood area and increasing the general imaging expertise of neuroscientists.



      Member: Ocaña, Michelle
      Role: Core Facility Manager, Senior Imaging Specialist
      Phone: (617) 432-1683


    Biological Specimens


    • BX63 Motorized Fluorescent Microscope ( Fluorescence microscope )

    • FV1000 Laser Scanning Confocal Microscope ( Laser scanning confocal microscope )

      "The FluoViewTM FV1000 is capable of simultaneous collection from up to 4 detection channels using multiple laser and conventional illumination sources. Wavelength selection and flexible control of laser intensity with advanced AOTF technology permits reduced specimen fading, lower crosstalk, and excitation area selection. Olympus confocal microscopes are ideal for 3-D imaging, time course experiments, energy transfer visualization, and photobleaching recovery experiments. This confocal has 4 PMTs, SIM scanner and spectral deconvolution. "

    • High powered analysis workstations with Arivis, Amira, Imaris, Huygens and Fiji ( Computer workstation )

    • LaVision Ultramicroscope II Light Sheet Microscope ( Fluorescence microscope )

      The bidirectional triple light sheet technology of the UltraMicroscope II generates 6 focused light sheets to excite samples from the side while the fluorescence light is detected by a sCMOS camera perpendicular to the illumination plane. Moving the sample through the light sheet generates a 3D image stack. Selective excitation of the focal plane reduces bleaching and photo toxicity significantly. The open setup allows the analysis of cleared samples in any clearing solution or in aqueous media. The dynamic horizontal light sheet focus guarantees excellent Z-resolution covering the entire field of view.

    • Leica SP8 X STED/FLIM ( Laser scanning confocal microscope )

      The Leica SP8 X is a high sensitivity confocal microscope system that offers complete flexibility for any fluorescence experiment.

      List of features include: white light laser, spectrophotometric detector, humidified stage top incubator, resonant scanner, large field of view, automated stage for confocal montage, motorized DIC, laser based autofocus, galvo-z, and HyD sentisitive detectors.

    • Leica SPE ( Confocal microscope )

      Provides all the features needed for routine confocal techniques; offering excellent image quality.
      Spectrophotometric detector - User definable emission bandwidths
      Automated stage for confocal montage images.
      Motorized DIC - Automatically inserts the correct DIC Prism, Polarizer, and Analyzer. The bias of the prism can be stored and applied automatically.
      Precise galvo-Z for quick Z-stack imaging.

    • MVX10 Macroview Dissecting Microscope ( Stereo microscope )

      "The MVX10 Optical concept: The MVX is a mono zoom microscope designed for fluorescence imaging. The MVX features a single zoom optical path with a large diameter, which is optimized to collect light with unprecedented efficiency and resolution at all its magnifications. The MVX gives the user maximum flexibility in observing the specimen without switching objectives. A series of parfocal objectives is also available along with a dual nosepiece. This allows the user to utilize the full zoom range of two objectives by easily rotating one or the other into the light path. Using the 0.63x and 2x objectives and 10x eyepieces on the MVX10 gives an effective zoom range of 4x to 126x, or a 31:1 ratio. This allows for field of view from 55mm to 1.74mm. "

    • Offline Workstations ( Computer )

      "Our current offline workstations are equipped with Metamorph analysis software for fast, accurate analysis. Visage Amira is also installed for 3D rendering and measurement."

    • STORM ( Fluorescence microscope )

      "The STORM microscope is built around an Olympus IX71 microscope mount and Olympus laser combiner and autofocus mechanism. The STORM microscope currently has two laser lines for covalently paired dyes, 543 and 640nm. The STORM microscope has the ability to resolve beyond the diffraction limits of a typical light microscope. Resolution is in the 20-60nm range."

    • TissueVision TissueCyte 2-photon tomography ( Optical microscope )

    • VivaView FL Incubator Fluorescence Microscope ( Fluorescence microscope )

      "The new VivaView FL incubator microscope from Olympus incorporates optimal cell growing conditions with proven imaging optics. Maintaining all the benefits associated with a dedicated incubator, the VivaView FL provides a fully integrated and motorized inverted microscope to allow high quality, long-term time-lapse imaging in a constant and optimized environment. Multiple locations in up to 8 samples can be imaged simultaneously with fluorescence or DIC. Simple, intuitive computer operation removes all the difficulty previously associated with configuring a live cell imaging system."

    • VS120 Slide Scanner ( Slide scanner )

      "The Olympus VS120 Whole Slide Scanner has been specifically designed for high throughput facilities that require fast scanning speed and high image resolution. The VS120-SL 5 Slide System holds 5 slides at a time making it quicker and easier to archive slides and produce permanent records. Virtual slide creation could not be simpler—just set the slide in place and press Start. Olympus Plan Apo 2x, 10x, 20x and 40x objectives are available."

    • VS120 Slide Scanner ( Slide scanner )

    • Zeiss COMBI System-Microdissection and optical tweezers ( Microdissection instrument )


    • Array Tomography (AT) Core ( Material analysis service )

      The Array Tomography Core (AT Core) provides high resolution 3D reconstruction of tissue below the diffraction limit. We circumvent this limitation through physical serial sectioning of tissue below the diffraction limit. That is, we embed tissue (usually murine brain) in LR White resin then use an ultramicrotome to serially section the tissue at ~70 nm. These tissue arrays are then probed using various antibodies specific to desired antigens, usually pre- and post-synaptic markers, via standard immunohistochemistry techniques. The stained arrays are then imaged using a widefield epifluorescent scope and the resulting images are aligned and the final 3D volume rendered in various software (Amira, ImageJ, Metamorph).

    • Imaging Equipment Access Service ( Access service )

      Instrumentation access provided to authorized researchers.

      "The Neurobiology Imaging Core Facility will provide training sessions for free. You will be expected to safely turn on and run the equipment and know the shutdown routine before you can use the equipment autonomously.

      Offline workstations loaded with Metamorph, Imaris, ImageJ and CellSens are provided for post-acquisition analysis.

      Long term data storage is not provided. Users must use their own collaboration folders on the HMS server or save their data on a personal device. Data over 1 month old will be deleted.

      PUBLICATION ACKNOWLEDGEMENT: If research supported by the Neurobiology Imaging Facility results in publication, please acknowledge this support by including the following statement in your publication(s):

      We thank the Neurobiology Department and the Neurobiology Imaging Facility for consultation and instrument availability that supported this work. This facility is supported in part by the Neural Imaging Center as part of an NINDS P30 Core Center grant #NS072030."

    • RNAscope ( Material modification service )

    • Tissue clearing ( Material modification service )

    • Whole organ scanning ( Material analysis service )

    • Whole slide scanning ( Material analysis service )


    • Amira VR ( Software )

    • Arivis ( Software )

    • Hyugens ( Software )

    • Imaris ( Software )

      "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."

    Web Links:

    Last updated: 2020-03-09T13:11:38.541-04:00

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