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Image and Data Analysis Core (HMS)

Director: Elliott, Hunter, Ph.D.

Location: Building LHRRB, Room 302, Harvard Medical School, 240 Longwood Ave., Boston, MA 02115

Summary:

IDAC provides image data analysis services to individual labs and core facilities at Harvard Medical School, including the ICCB-Longwood Screening Facility (ICCB-L), the Drosophila RNAi Screening Center (DRSC), and the Nikon Imaging Center (NIC).

Affiliations:

People:

Resources:

Services

  • Computational image data analysis ( Data analysis service )

    Our mission:

    - Maintain, deploy, and expand collection of methods for computational image data analysis (in-house and commercial)
    - Provide expertise in assembling individual methods into complete processing pipelines for specific projects
    - Interface image data analysis with HMS high-performance computing infrastructure
    - Provide intellectual environment for the creation of new methods and processing pipelines

Software

  • Amira ( Software )

  • Biosensor Processing Software 2.1 ( Software )

    "This matlab software package allows processing of raw ratiometric biosensor images into fully corrected 'ratio maps' or 'activation maps' — images showing the localized activation of the biosensor. This includes application of all necessary image corrections needed for quantitative widefield imaging of ratiometric biosensors."

    Available through the Gaudenz Danuser lab.

  • CellProfiler ( Algorithmic software suite )

    "CellProfiler is free open-source software designed to enable biologists without training in computer vision or programming to quantitatively measure phenotypes from thousands of images automatically. See our papers on analyzing cell images and non-cell images."

    Available through the Broad Institute.

  • ClusterTracker ( Software )

    "ClusterTrack is the Matlab software developed for the purpose of proving the principle that full microtubule dynamics can be tracked and inferred based on +TIP marker live cell image sequences only. The download bundle contains the Matlab programs documented by a software guide. It also contains multi-color movies of EGFP-EB1 and mCherry-tubulin used for validation. Note, this package will not be maintained and it is not set up as a user–friendly software. We strongly recommend the download of the plusTipTracker package for practical microtubule analyses."

    Available through the Gaudenz Danuser lab.

  • Fiji/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."

    Available through the NIH.

  • Fiji/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."

    Available through the NIH.

  • 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."

  • 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."

  • MATLAB ( Software )

    "MATLAB® is a high-level language and interactive environment that enables you to perform computationally intensive tasks faster than with traditional programming languages such as C, C++, and Fortran."

    Available through RITG.

  • 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 for over 25 years."

  • Metamorph NX ( Software )

  • plusTipTracker ( Software )

    "plusTipTracker is a Matlab software package for tracking the full dynamics of microtubules based on +TIP marker live cell image sequences. Concepts are related to the ClusterTrack software; however, the tracking builds on the algorithms implemented in the u-track software. The package can be operated via a convenient graphical user interface. It contains a sizable set of service functions for data visualization and statistical processing of parameters of microtubule dynamics. We strongly recommend the download of this package for the purpose of microtubule tracking. The download bundle includes a user's guide in the form of a Technical Report and complete documentation of all the functions in the package."

    Available through the Gaudenz Danuser lab.

  • u-track ( Software )

    "u-track is a multiple-particle tracking Matlab software that is designed to (1) track dense particle fields, (2) close gaps in particle trajectories resulting from detection failure, and (3) capture particle merging and splitting events resulting from occlusion or genuine aggregation and dissociation events. Its core is based on formulating correspondence problems as linear assignment problems and searching for a globally optimal solution."

    Available through the Gaudenz Danuser lab.


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Last updated: 2015-12-03T15:41:41.681-06:00

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