Free Image Analysis Tools
ImageJ is a free public domain image processing program developed at the NIH. Downloadable distributions are available for Windows, Mac OS, Mac OS X and Linux.
Documentation, plugins and archive of the mailing list are available at the ImageJ website,
Fiji is a free image processing package. It can be described as a distribution of ImageJ together with Java, Java 3D and a lot of plugins organized into a coherent menu structure
CellProfiler is a free open-source software for measuring and analyzing cell images developed at the Broad Institute. The website includes tutorials, examples and documentation as well as a user forum.
VirtualDub is a free video capture/processing utility for Windows platforms. It is mainly geared toward processing AVI files, although it can read (not write) MPEG-1 and also handle sets of BMP images.
Documentation and user forum are available online.
ZEISS LSM Image Browser is a free browser for LSM files.
Zen Imaging Software is a modular image-processing and analysis software for modern microscopy from by Carl Zeiss. The basic version (lite) is free.
Commercial Image Analysis Tools
Imaris is a 3D-4D Visualization and Image Analysis software by Bitplane.
The Biological Services Unit provides floating license. Contact Us for further instructions.
Video Tutorials, Case Studies, How to... and FAQ are availiable online.
Volocity is a 3D-4D imaging software by Perkin Elmer. The Biological Services Unit provides a campus license. You may download Volocity, at no cost. Contact Us for further instructions.
User Manual, tutorials, hints and tips are available online.
Avizo is a sophisticated and flexible software package by VSG for 3D visualization of data arising in many scientific areas, including biology, geology, atmospheric science, fluid dynamics, and others. Avizo can also serve as a graphical front-end to Matlab. Users of Amira will find it very familiar.
The Electron Microscopy Unit provides a campus license. Contact us for license details. You can subscribe avizousers mailing list at WIS.
Documentation, user forum, video tutorials and a list of supported formats are available online.
Matlab high level programming language has extensive built-in tools for image and data analysis.
WIS has a campus license. An introductory course on Matlab and Data Analysis is given at the Feinberg Gradute School on both semesters in the current year.
Matlab Central hosts a File Exchange and Newsgroup and should be your first point for searching help on top of the software built-in documentation.
Caltech's course on Image analysis for biology gives a thourough introduction to image analysis using matlab.
Optical Imaging
Living Image by Caliper Life Sciences, is a software for IVIS® in vivo imaging systems. It features advanced spectral unmixing tools to enhance fluorescent sensitivity and automated 3D image acquisition and analysis providing an anatomical view of disease activity and drug efficacy.
WIS has a campus license. You may download the latest Living Image software at no cost. Contact Us for further instructions.
The latest Installation Guide, and User Guide are available online.
Digital Pathology
Panoramic Viewer is a free tool for Visualization and Annotation of digital slides acquired using the Panoramic MIDI digital slides scanner.
HistoQuant is a quantitative and qualitative analysis module for both tissue samples and cells. It is installed on the Image Analysis workstation at the Biological Services Unit.
MRI
MRIcro is a free tool which allows Windows and Linux computers view medical images. It is a standalone program, but includes tools to complement SPM (software that allows neuroimagers to analyse MRI, fMRI and PET images). MRIcro allows efficient viewing and exporting of brain images. In addition, it allows neuropsychologists to identify regions of interest (ROIs, e.g. lesions). MRIcro can create Analyze format headers for exporting brain images to other platforms.
SPIN – is a free windows based software for signal processing in NMR. SPIN deals with the processing for a number of MRI sequences such as: SWI, PWI, MR angiography (MRA), dynamic contrast enhanced imaging (DCE), special image processing features such as interpolation and other mathematical operations, and special features for ease of use by clinicians. It can handle different image formats and has strong 3D view capabilities.
mriMaps is a software application for analysis and display of MRI data. It was developed in collaboration with Prof. Michal Neeman, Dr. Hagit Dafni and Reut Avni from the department of Biological Regulation. Contact us for more information
SPM Toolbox
Osirix – Mac only
EM
IMod is a set of image processing, modeling and display programs used for tomographic reconstruction and for 3D reconstruction of EM serial sections and optical sections. IMOD was developed at the Boulder Laboratory for 3-D Electron Microscopy of Cells and the Regents of the University of Colorado.
Bsoft is a collection of programs and a platform for development of software for image and molecular processing in structural biology
EMAN is a suite of scientific image processing tools aimed primarily at the transmission electron microscopy community, though it is beginning to be used in other fields as well.”