eagle-i Harvard UniversityHarvard University
See it in Search

Optical Microscopy Core (PCMM @ Children’s Hospital Boston)

Location: 200 Longwood Ave., WAB Rooms 175 and 274A, Boston, MA 02115, 3 Blackfan Circle, 3rd/Fl, Room 3123, Boston, MA 02115


Confocal and multiphoton are modern fluorescence techniques in microscopy for generating optical sections from live or fixed biological specimens. In general, both techniques employ a point scanning and point detecting design. The confocal microscope achieves point detection by using a confocal pinhole to block off out-of-focus emission from the specimen. The multiphoton microscope, on the other hand, generates intrinsic point emission directly from the in-focus spot, thereby eliminating the need for a confocal pinhole. Subsequent scanning of the entire field of view results in an optical section. Computer reconstruction of serial optical sections, collected at consecutive axial (z) positions, can reveal the spatial localization of cells and tissues (sometime subcellular molecules) in 3D. The ability to see biochemical processes in live cells, in real time, sheds light on the vastly complex molecular world of cells and may allow IDI scientists to identify new targets for drugs that will treat exposure to dangerous toxins and bacteria as well as fight a wide variety of diseases.





    • Marianas SDC system, with Yokogawa CSU22 Spinning Disk ( Spinning-disk confocal microscope )

      "The 3i Marianas™ system represents the ultimate inverted digital microscopy workstation. Marianas is composed of state-of-the-art optics, opto-electronics, CCD cameras, software and computers tailored for your specific application. Marianas fully integrates with SlideBook software. Marianas is equipped for both live and fixed cell widefield epifluorescence applications as well as transmitted illumination techniques."

    • Olympus Fluoview FV1000 confocal system ( Confocal microscope )

      "Olympus FluoView FV1000 is designed for high-resolution, confocal observation of both fixed and living cells. The FV1000 offers advances in confocal system performance while providing the speed and sensitivity required for live cell imaging, with minimal risk of damage to living specimens.

      In addition, the FV1000 offers a revolutionary synchronized laser scanning system called the SIM Scanner. While one laser stimulates, the second laser simultaneously provides high-resolution imaging. This coordination of laser stimulation and imaging makes the FV1000 an ideal choice for FRAP, FLIP and photoactivation."

    • Olympus FV1200 MPE multiphoton system ( Two-photon confocal microscope )


    • Microscope access service ( Access service )

      "All of the microscopes at the IDI Microscopy Core are shared equipment and are available to both internal and outside users. However, IDI users are given priority."

    • Microscope training service ( Training service )

      "Training is required for use of any Core equipment. In general, five to six hours hands on training will be required for unsupervised operation of most microscopes. A user must show proficiency in operation of a particular instrument before they will be given access to the scheduling calendar to book their own time. For further information and to request training, please contact the Core Manager."


    • AutoDeblur ( Software )

      "AutoDeblur is the life science industry’s leading image deconvolution software. It offers the most complete suite of 2D and 3D algorithms available, including the industry’s only "Blind Deconvolution" algorithm. AutoDeblur delivers superior precision and accuracy while preserving data integrity. It is effective with all current optical microscopes including wide-field fluorescence, confocal (CLSM and SDC), transmitted light brightfield, multiple-photon and DIC. "

    • Confocal Assistant ( Software )

      "Software for 3D analysis of confocal images. Version has not changed since 1996, but still runs well on most Windows platforms."

    • ImageJ ( Software )

      "ImageJ is a public domain Java image processing program inspired by NIH Image for the Macintosh. It runs, either as an online applet or as a downloadable application, on any computer with a Java 1.4 or later virtual machine. Downloadable distributions are available for Windows, Mac OS, Mac OS X and Linux.

      It can display, edit, analyze, process, save and print 8-bit, 16-bit and 32-bit images. It can read many image formats including TIFF, GIF, JPEG, BMP, DICOM, FITS and "raw". It supports "stacks", a series of images that share a single window. It is multithreaded, so time-consuming operations such as image file reading can be performed in parallel with other operations.

      It can calculate area and pixel value statistics of user-defined selections. It can measure distances and angles. It can create density histograms and line profile plots. It supports standard image processing functions such as contrast manipulation, sharpening, smoothing, edge detection and median filtering."

    • 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."

    • Lasersharp ( Software )

    • SlideBook ( Software )

      "Comprehensive digital microscopy imaging software."

    • Volocity ( Software )

      "High Performance 3D-4D imaging software for a better insight to your science."

    • VoxBlast ( Software )

    Web Links:

    Last updated: 2018-04-19T15:55:34.681-04:00

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